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Onate-Quiroz KV, Nwosu BU, Salemi P. Novel duplication of the cell adhesion molecule L1-like gene in an individual with cognitive impairment, tall stature, and obesity: A case report. Front Neurol 2023; 14:1104649. [PMID: 37114233 PMCID: PMC10126371 DOI: 10.3389/fneur.2023.1104649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
The gene that codes for the close homolog of L1 (CHL1 gene) is located in the 3p26.3 cytogenetic band in the distal portion of the 3p chromosome. This gene is highly expressed in the central nervous system and plays an important role in brain formation and plasticity. Complete or partial CHL 1 gene-deficient mice have demonstrated neurocognitive deficits. In humans, mutations of the CHL 1 gene are infrequent with most mutations described in the literature as deletions. This case report describes an individual with a duplication in the CHL 1 and a presentation consistent with a syndromic form of neurocognitive impairment. To the best of our knowledge, this mutation has not been previously described in the literature.
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Morisawa K, Sato T, Shimoyamada M, Mizuno R, Ohashi H, Watanabe-Hisazumi H, Takeshima K, Kojima A, Sato S, Hasegawa T, Takahashi T. Adapted whole-body surveillance for von Hippel-Lindau-associated tumors in 3p deletion syndrome with VHL deletion: A case report. Pediatr Blood Cancer 2022; 69:e29732. [PMID: 35441425 DOI: 10.1002/pbc.29732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/28/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Kazumi Morisawa
- Department of Pediatrics, Saitama City Hospital, Saitama, Japan.,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Sato
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | | | - Ryuichi Mizuno
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | | | | | - Atsuhiro Kojima
- Department of Neurosurgery, Saitama City Hospital, Saitama, Japan
| | - Seiji Sato
- Department of Pediatrics, Saitama City Hospital, Saitama, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Takao Takahashi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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Eisfeldt J, Rezayee F, Pettersson M, Lagerstedt K, Malmgren H, Falk A, Grigelioniene G, Lindstrand A. Multi-omics analysis reveals multiple mechanisms causing Prader-Willi like syndrome in a family with a X;15 translocation. Hum Mutat 2022; 43:1567-1575. [PMID: 35842787 PMCID: PMC9796698 DOI: 10.1002/humu.24440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 01/07/2023]
Abstract
Prader-Willi syndrome (PWS; MIM# 176270) is a neurodevelopmental disorder caused by the loss of expression of paternally imprinted genes within the PWS region located on 15q11.2. It is usually caused by either maternal uniparental disomy of chromosome 15 (UPD15) or 15q11.2 recurrent deletion(s). Here, we report a healthy carrier of a balanced X;15 translocation and her two daughters, both with the karyotype 45,X,der(X)t(X;15)(p22;q11.2),-15. Both daughters display symptoms consistent with haploinsufficiency of the SHOX gene and PWS. We explored the architecture of the derivative chromosomes and investigated effects on gene expression in patient-derived neural cells. First, a multiplex ligation-dependent probe amplification methylation assay was used to determine the methylation status of the PWS-region revealing maternal UPD15 in daughter 2, explaining her clinical symptoms. Next, short read whole genome sequencing and 10X genomics linked read sequencing was used to pinpoint the exact breakpoints of the translocation. Finally, we performed transcriptome sequencing on neuroepithelial stem cells from the mother and from daughter 1 and observed biallelic expression of genes in the PWS region (including SNRPN) in daughter 1. In summary, our multi-omics analysis highlights two different PWS mechanisms in one family and provide an example of how structural variation can affect imprinting through long-range interactions.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden,Science for Life LaboratoryKarolinska Institutet Science ParkSolnaSweden
| | - Fatemah Rezayee
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
| | - Maria Pettersson
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
| | - Kristina Lagerstedt
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
| | - Helena Malmgren
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
| | - Anna Falk
- Department of NeuroscienceKarolinska InstituteStockholmSweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
| | - Anna Lindstrand
- Department of Molecular Medicine and SurgeryKarolinska InstitutetSolnaSweden,Department of Clinical GeneticsKarolinska University HospitalStockholmSweden
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Findley TO, Crain AK, Mahajan S, Deniwar A, Davis J, Solis Zavala AS, Corno AF, Rodriguez-Buritica D. Congenital heart defects and copy number variants associated with neurodevelopmental impairment. Am J Med Genet A 2021; 188:13-23. [PMID: 34472185 DOI: 10.1002/ajmg.a.62484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/21/2023]
Abstract
A genetic etiology is identifiable in 20%-30% of patients with congenital heart defects (CHD). Chromosomal microarray analysis (CMA) can detect copy number variants (CNV) associated with CHD. In previous studies, the diagnostic yield of postnatal CMA testing ranged from 4% to 28% in CHD patients. However, incidental pathogenic CNV and variants of unknown significance are often discovered without any known association with CHD. The study objective was to describe the rate of pathogenic CNV associated with neurodevelopmental impairment (NDI) and compare clinical findings in CHD neonates with genetic results. A single-center retrospective review was performed on all consecutive newborns with CHD admitted to a tertiary neonatal intensive care unit from January 2013 to March 2019 (n = 525). CHD phenotypes were classified as per the National Birth Defect Prevention Study. CMA detected pathogenic CNV in 21.3% (61/287) of neonates, and karyotype or fluorescence in situ hybridization detected aneuploidies in an additional 11% of the overall cohort (58/525). Atrioventricular septal defects and conotruncal defects showed the highest diagnostic yield by CMA (28.6% and 27.2%, respectively). Among neonates with pathogenic CNV on CMA, 78.7% (48/61) were associated with NDI. Neonates with pathogenic CNV were smaller in length at birth compared to those with benign CNV or variants of unknown significance (p = 0.005) and were more likely to be discharged with an enteral feeding tube (p = 0.027). CMA can discover genetic variants associated with NDI and are common in neonates with CHD. Genetic testing in the neonatal period can heighten awareness of genetic risk for NDI.
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Affiliation(s)
- Tina O Findley
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Alyssa K Crain
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Smridhi Mahajan
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ahmed Deniwar
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Children's Heart Institute, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jessica Davis
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ana S Solis Zavala
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Antonio F Corno
- Children's Heart Institute, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - David Rodriguez-Buritica
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, USA
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5
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Lu S, Wei X, Chen B, Chen J, Zhang L, Yang M, Sun Z, Shi Y, Kong Y, Liu S, Li Y. A new phenomenon of cochlear otosclerosis: an acquired or congenital disease? - A clinical report of cochlear otosclerosis. Acta Otolaryngol 2021; 141:551-556. [PMID: 33819124 DOI: 10.1080/00016489.2021.1906947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND No cochlear otosclerosis in infants with congenital bilateral SNHL has been reported. AIMS/OBJECTIVES We report an infant male with bilateral cochlear otosclerosis, suggesting that cochlear otosclerosis may be a congenital disease and to further analyze the etiology of and genetic expression in congenital bilateral cochlear otosclerosis. We also describe the clinical characteristics and experience of patients with bilateral cochlear otosclerosis treated with cochlear implants (CIs). MATERIALS AND METHODS Seven patients, including an infant, who were diagnosed with cochlear otosclerosis underwent CI surgery. Their medical records, audiological and radiological results, surgical procedures, and CI outcomes were collected and reviewed. RESULTS The median age at hearing loss was 38 years, ranging from 0 to 47 years. The child had bilateral hearing loss at birth and received a CI at 1 year of age. He also had growth retardation and was diagnosed with 3q+/3p- syndrome. All patients (8 ears) had better postoperative auditory performance than that preoperatively. CONCLUSIONS AND SIGNIFICANCE Although cochlear otosclerosis often starts at middle age and progresses slowly, it may be a congenital disease that is related to chromosome abnormality. This disease presents with SNHL or MHL, and treatment with a CI is beneficial.
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Affiliation(s)
- Simeng Lu
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Xingmei Wei
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Biao Chen
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Jingyuan Chen
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Lifang Zhang
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Mengge Yang
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Zhiming Sun
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Ying Shi
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
| | - Ying Kong
- Beijing Institute of Otolaryngology, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
| | - Sha Liu
- Beijing Institute of Otolaryngology, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
| | - Yongxin Li
- Department of Otorhinolaryngology and Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, P. R. China
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Novel Variants in Hearing Loss Genes and Associations With Audiometric Thresholds in a Multi-ethnic Cohort of US Patients With Cochlear Implants. Otol Neurotol 2021; 41:978-985. [PMID: 32658404 DOI: 10.1097/mao.0000000000002671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To investigate novel variants in hearing loss genes and clinical factors affecting audiometric outcomes of cochlear implant (CI) patients. BACKGROUND Approximately 50% of hearing loss has a genetic etiology, with certain genetic variants more prevalent in specific ethnic groups. Different variants and some clinical variables including inner ear malformations result in different prognoses or clinical outcomes after CI. METHODS Medical and genetic testing records of pediatric CI patients were reviewed for clinical variables. Minor allele frequencies of variants were obtained from Genome Aggregation Database (gnomAD) and variants were classified for pathogenicity. Standard statistical testing was done using Fisher's exact, Wilcoxon, and Spearman correlation tests. RESULTS Eighteen CI patients with genetic test results had pathogenic variants, including six patients with syndromic hearing loss and six patients with known GJB2 variants. Novel pathogenic variants were noted in CHD7, ADGRV1, and ARID1B, with variants in the latter two genes identified in Hispanic patients. Overall, carriage of genetic variants was associated with better pre-CI audiometric thresholds at 2000 Hz (p = 0.048). On the other hand, post-CI thresholds were significantly worse in patients with inner ear malformations, particularly in patients with atretic cochlear nerve canals. CONCLUSION Four novel pathogenic variants were identified, which contributes to knowledge of allelic spectrum for hearing loss especially in Hispanic patients. In this cohort, carriage of pathogenic variants particularly of GJB2 variants was associated with better pre-CI audiometric thresholds, while patients with inner ear malformations had worse post-CI audiometric thresholds.
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Fetal Cystic Hygroma Associated with Terminal 2p25.1 Duplication and Terminal 3p25.3 Deletion: Cytogenetic, Fluorescent in Situ Hybridization and Microarray Familial Characterization of Two Different Chromosomal Structural Rearrangements. Balkan J Med Genet 2021; 23:79-86. [PMID: 33816076 PMCID: PMC8009571 DOI: 10.2478/bjmg-2020-0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We report a prenatally diagnosed case of partial trisomy 2p and partial monosomy 3p, resulting from unbalanced translocation (2;3)(p25.1;p25.3) of paternal origin. Parents were non consanguineous Caucasians, with familial history of recurrent miscarriages on the father’s side. Detailed sonographic examination of the fetus showed a septated cystic hygroma measuring 6 mm at 13 weeks’ gestation. Karyotyping and fluorescent in situ hybridization (FISH) analysis of cultured amniotic fluid cells revealed an unbalanced translocation der(3)t(2;3)(p25.1; p25.3) and apparently balanced inv(3)(p13p25.3) in a fetus. Parental cytogenetic evaluation using karyotyping and FISH analysis showed the presence of both a balanced translocation and a paracentric inversion in father t(2;3) (p25.1;p25.3) inv(3)(p13p25.3). Microarray analysis showed a 11.6 Mb deletion at 3p26.3-p25.3 and duplication of 10.5 Mb at the 2p25.3-p25 region. The duplicated region at 2p25.1p25.3 contains 45 different genes, where 12 are reported as OMIM morbid genes with different phenotypical implications. The deleted region at 3p26.3-p25.3 contains 65 genes, out of which 27 are OMIM genes. Three of these (CNTN4, SETD5 and VHL) were curated by Clingene Dosage Gene Map and were given a high haplo-insufficiency score. Genes affected by the unbalanced translocation could have contributed to some specific phenotypic changes of the fetus in late pregnancy. The application of different cytogenetic methods was essential in our case, allowing the detection of different types of structural chromosomal aberrations and more thorough genetic counseling for future pregnancies.
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Gandawijaya J, Bamford RA, Burbach JPH, Oguro-Ando A. Cell Adhesion Molecules Involved in Neurodevelopmental Pathways Implicated in 3p-Deletion Syndrome and Autism Spectrum Disorder. Front Cell Neurosci 2021; 14:611379. [PMID: 33519384 PMCID: PMC7838543 DOI: 10.3389/fncel.2020.611379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is characterized by impaired social interaction, language delay and repetitive or restrictive behaviors. With increasing prevalence, ASD is currently estimated to affect 0.5–2.0% of the global population. However, its etiology remains unclear due to high genetic and phenotypic heterogeneity. Copy number variations (CNVs) are implicated in several forms of syndromic ASD and have been demonstrated to contribute toward ASD development by altering gene dosage and expression. Increasing evidence points toward the p-arm of chromosome 3 (chromosome 3p) as an ASD risk locus. Deletions occurring at chromosome 3p result in 3p-deletion syndrome (Del3p), a rare genetic disorder characterized by developmental delay, intellectual disability, facial dysmorphisms and often, ASD or ASD-associated behaviors. Therefore, we hypothesize that overlapping molecular mechanisms underlie the pathogenesis of Del3p and ASD. To investigate which genes encoded in chromosome 3p could contribute toward Del3p and ASD, we performed a comprehensive literature review and collated reports investigating the phenotypes of individuals with chromosome 3p CNVs. We observe that high frequencies of CNVs occur in the 3p26.3 region, the terminal cytoband of chromosome 3p. This suggests that CNVs disrupting genes encoded within the 3p26.3 region are likely to contribute toward the neurodevelopmental phenotypes observed in individuals affected by Del3p. The 3p26.3 region contains three consecutive genes encoding closely related neuronal immunoglobulin cell adhesion molecules (IgCAMs): Close Homolog of L1 (CHL1), Contactin-6 (CNTN6), and Contactin-4 (CNTN4). CNVs disrupting these neuronal IgCAMs may contribute toward ASD phenotypes as they have been associated with key roles in neurodevelopment. CHL1, CNTN6, and CNTN4 have been observed to promote neurogenesis and neuronal survival, and regulate neuritogenesis and synaptic function. Furthermore, there is evidence that these neuronal IgCAMs possess overlapping interactomes and participate in common signaling pathways regulating axon guidance. Notably, mouse models deficient for these neuronal IgCAMs do not display strong deficits in axonal migration or behavioral phenotypes, which is in contrast to the pronounced defects in neuritogenesis and axon guidance observed in vitro. This suggests that when CHL1, CNTN6, or CNTN4 function is disrupted by CNVs, other neuronal IgCAMs may suppress behavioral phenotypes by compensating for the loss of function.
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Affiliation(s)
- Josan Gandawijaya
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - J Peter H Burbach
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Fu J, Wang T, Fu Z, Li T, Zhang X, Zhao J, Yang G. Case Report: A Case Report and Literature Review of 3p Deletion Syndrome. Front Pediatr 2021; 9:618059. [PMID: 33643973 PMCID: PMC7902511 DOI: 10.3389/fped.2021.618059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: The aim of the present study is to explore the clinical and genetic characteristics of 3p deletion syndrome to improve clinicians' understanding of the disease. Methods: The clinical manifestations, process of diagnosis and treatment, and genetic characteristics of an individual case of 3p deletion syndrome were analyzed. CNKI, Wanfang Data, and the Biomedical Literature Database (PubMed) were searched. The search time limit, using "3p deletion syndrome" and "BRPF1" as keywords, was from the creation of the database up to June 2020. Related data were reviewed. Results: The proband was a male child with general developmental and intellectual disabilities, special facial features and congenital heart disease. The child was the parents' first pregnancy and first born. Gene microarray analysis showed a 10.095 Mb deletion in the 3p26.3-p25.3 region, resulting in a heterozygous mutation of the BRPF1 gene; thus, the patient was diagnosed with 3p deletion syndrome. At the time of diagnosis, the child was 1 year of age and was responding to comprehensive rehabilitation training. A total of 29 well-documented cases were found in the literature, of which 19 cases had an onset within 1 year of birth, and mainly manifested with mental and motor development disabilities and abnormal facial features, with different gene deletions, depending on the size and location of the 3p deletion. Conclusion: The genetic test results of the child in this study indicated a heterozygous deletion of the BRPF1 gene on the short arm of chromosome 3, which was a unique feature of this study, since it was rarely mentioned in other reports of 3p deletion syndrome. The clinical phenotype of this syndrome is complex as it can include intellectual and motor development backwardness, low muscle tone, certain abnormal facial features (low hairline, bilateral ptosis, widely spaced eyes, a forward nose, left ear auricle deformity, a high-arched palate, a small jaw), and the deformation of systems such as the gastrointestinal tract and the urinary tract malformation or symptoms of epilepsy. As clinical manifestations can be relatively mild, the syndrome is easy to miss or misdiagnose. Clinical workers need to be aware of this disease when they find that children have special features, such as stunted growth, low muscle tone or ptosis, and it needs to be diagnosed through genetic testing. Most children are able to develop certain social skills after rehabilitation treatment.
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Affiliation(s)
- Junxian Fu
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ting Wang
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhuo Fu
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Tianxia Li
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Xiaomeng Zhang
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Jingjing Zhao
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Guanglu Yang
- Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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10
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Smits JJ, Oostrik J, Beynon AJ, Kant SG, de Koning Gans PAM, Rotteveel LJC, Klein Wassink-Ruiter JS, Free RH, Maas SM, van de Kamp J, Merkus P, Koole W, Feenstra I, Admiraal RJC, Lanting CP, Schraders M, Yntema HG, Pennings RJE, Kremer H. De novo and inherited loss-of-function variants of ATP2B2 are associated with rapidly progressive hearing impairment. Hum Genet 2018; 138:61-72. [PMID: 30535804 PMCID: PMC6514080 DOI: 10.1007/s00439-018-1965-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/30/2018] [Indexed: 01/21/2023]
Abstract
ATP2B2 encodes the PMCA2 Ca2+ pump that plays an important role in maintaining ion homeostasis in hair cells among others by extrusion of Ca2+ from the stereocilia to the endolymph. Several mouse models have been described for this gene; mice heterozygous for loss-of-function defects display a rapidly progressive high-frequency hearing impairment. Up to now ATP2B2 has only been reported as a modifier, or in a digenic mechanism with CDH23 for hearing impairment in humans. Whole exome sequencing in hearing impaired index cases of Dutch and Polish origins revealed five novel heterozygous (predicted to be) loss-of-function variants of ATP2B2. Two variants, c.1963G>T (p.Glu655*) and c.955delG (p.Ala319fs), occurred de novo. Three variants c.397+1G>A (p.?), c.1998C>A (p.Cys666*), and c.2329C>T (p.Arg777*), were identified in families with an autosomal dominant inheritance pattern of hearing impairment. After normal newborn hearing screening, a rapidly progressive high-frequency hearing impairment was diagnosed at the age of about 3–6 years. Subjects had no balance complaints and vestibular testing did not yield abnormalities. There was no evidence for retrocochlear pathology or structural inner ear abnormalities. Although a digenic inheritance pattern of hearing impairment has been reported for heterozygous missense variants of ATP2B2 and CDH23, our findings indicate a monogenic cause of hearing impairment in cases with loss-of-function variants of ATP2B2.
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Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andy J Beynon
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pia A M de Koning Gans
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Rolien H Free
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Groningen, Groningen, The Netherlands
| | - Saskia M Maas
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jiddeke van de Kamp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Paul Merkus
- Department of Otolaryngology, Head and Neck Surgery, Ear and Hearing, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Koole
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margit Schraders
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Helger G Yntema
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
- Hearing and Genes, Department of Human Genetics, Radboud University Medical Center, Internal postal code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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11
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Li C, Liu C, Zhou B, Hu C, Xu X. Novel microduplication of CHL1 gene in a patient with autism spectrum disorder: a case report and a brief literature review. Mol Cytogenet 2016; 9:51. [PMID: 27354858 PMCID: PMC4924281 DOI: 10.1186/s13039-016-0261-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/23/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The cell adhesion molecule L1-like (CHL1 or CALL) gene is located on chromosome 3p26.3, and it is highly expressed in the central and peripheral nervous systems. The protein encoded by this gene is a member of the L1 family of neural cell adhesion molecules, and it plays a role in nervous system development and synaptic plasticity. Moreover, studies of mice have revealed that CHL1 is a prime candidate gene for a dosage-sensitive autosomal form of mental retardation. To date, four patients with a microdeletion and two with a microduplication of 3p26.3 encompassing only the CHL1 gene have been reported in literature. CASE PRESENTATION In the present study, we have described a 16-month-old boy with autism spectrum disorder (ASD), developmental delay and minor dysmorphic facial features. This is the first report of a duplication of 3p26.3 including only the CHL1 gene in an ASD patient, and this duplication is the smallest reported to date in this gene. We also reviewed CHL1 gene mutation cases and examined whether this gene has an important role in cognitive function. CONCLUSIONS We conclude that both CHL1 deletions and duplications are likely responsible for the patient's impaired cognitive function, and CHL1 may be an intriguing ASD candidate gene.
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Affiliation(s)
- Chunyang Li
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai, China
| | - Chunxue Liu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai, China
| | - Bingrui Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai, China
| | - Chunchun Hu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai, China
| | - Xiu Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai, China
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12
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Zhang K, Song F, Zhang D, Liu Y, Zhang H, Wang Y, Dong R, Zhang Y, Liu Y, Gai Z. Chromosome r(3)(p25.3q29) in a Patient with Developmental Delay and Congenital Heart Defects: A Case Report and a Brief Literature Review. Cytogenet Genome Res 2016; 148:6-13. [PMID: 27077748 DOI: 10.1159/000445273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 11/19/2022] Open
Abstract
Ring chromosome 3, r(3), is an extremely rare cytogenetic abnormality with clinical heterogeneity and only 12 cases reported in the literature. Here, we report a 1-year-old girl presenting distinctive facial features, developmental delay, and congenital heart defects with r(3) and a ∼10-Mb deletion of chromosome 3pterp25.3 (61,891-9,979,408) involving 42 known genes which was detected using G-banding karyotyping and CytoScan 750K-Array. The breakpoints in r(3) were mapped at 3p25.3 and 3q29. We also analyzed the available information on the clinical features of the reported cases with r(3) and 3p deletion syndrome in order to provide more valuable information of genotype-phenotype correlations. To our knowledge, this is the largest detected fragment described in r(3) cases and the second r(3) study using whole-genome microarray.
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Affiliation(s)
- Kaihui Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
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13
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Suzuki-Muromoto S, Hino-Fukuyo N, Haginoya K, Kikuchi A, Sato H, Sato Y, Nakayama T, Kubota Y, Kakisaka Y, Uematsu M, Kumabe T, Kure S. A case of 3p deletion syndrome associated with cerebellar hemangioblastoma. Brain Dev 2016; 38:257-60. [PMID: 26365017 DOI: 10.1016/j.braindev.2015.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/06/2015] [Accepted: 07/23/2015] [Indexed: 10/23/2022]
Abstract
We described clinical course of a 24-year-old woman with 3p deletion syndrome associated with cerebellar hemangioblastoma at the age of 16 years old. She presented dysmorphic facial features, growth retardation and severe psychomotor retardation associated with 3p deletion syndrome. We identified de novo 3p deletion encompassing p25 by using array-based comparative genomic hybridization, where causative gene of von Hippel-Lindau (VHL) disease located. Surgical therapy for cerebellar hemangioblastoma was performed, and histological examination was consistent in cerebellar hemangioblastoma. She showed no other tumors associated VHL disease till 24 years old. This is the first case report of a patient with 3p deletion syndrome whose cerebellar hemangioblastoma may be associated with VHL disease. Repeat imaging studies were recommended for the patients with 3p deletion syndrome.
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Affiliation(s)
| | - Naomi Hino-Fukuyo
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan; Center for Genomic Medicine, Tohoku University Hospital, Sendai, Japan.
| | - Kazuhiro Haginoya
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan; Department of Pediatric Neurology, Takuto Rehabilitation Center for Children, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Hiroki Sato
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yuko Sato
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Tojo Nakayama
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yuki Kubota
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yosuke Kakisaka
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Mitsugu Uematsu
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Toshihiro Kumabe
- (d)Department of Neurosurgery, Tohoku University School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
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14
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Iype T, Alakbarzade V, Iype M, Singh R, Sreekantan-Nair A, Chioza BA, Mohapatra TM, Baple EL, Patton MA, Warner TT, Proukakis C, Kulkarni A, Crosby AH. A large Indian family with rearrangement of chromosome 4p16 and 3p26.3 and divergent clinical presentations. BMC MEDICAL GENETICS 2015; 16:104. [PMID: 26554554 PMCID: PMC4641370 DOI: 10.1186/s12881-015-0251-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/04/2015] [Indexed: 12/03/2022]
Abstract
Background The deletion of the chromosome 4p16.3 Wolf-Hirschhorn syndrome critical region (WHSCR-2) typically results in a characteristic facial appearance, varying intellectual disability, stereotypies and prenatal onset of growth retardation, while gains of the same chromosomal region result in a more variable degree of intellectual deficit and dysmorphism. Similarly the phenotype of individuals with terminal deletions of distal chromosome 3p (3p deletion syndrome) varies from mild to severe intellectual deficit, micro- and trigonocephaly, and a distinct facial appearance. Methods and results We investigated a large Indian five-generation pedigree with ten affected family members in which chromosomal microarray and fluorescence in situ hybridization analyses disclosed a complex rearrangement involving chromosomal subregions 4p16.1 and 3p26.3 resulting in a 4p16.1 deletion and 3p26.3 microduplication in three individuals, and a 4p16.1 duplication and 3p26.3 microdeletion in seven individuals. A typical clinical presentation of WHS was observed in all three cases with 4p16.1 deletion and 3p26.3 microduplication. Individuals with a 4p16.1 duplication and 3p26.3 microdeletion demonstrated a range of clinical features including typical 3p microdeletion or 4p partial trisomy syndrome to more severe neurodevelopmental delay with distinct dysmorphic features. Conclusion We present the largest pedigree with complex t(4p;3p) chromosomal rearrangements and diverse clinical outcomes including Wolf Hirschorn-, 3p deletion-, and 4p duplication syndrome amongst affected individuals. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0251-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Iype
- Department of Neurology, Government Medical College, Thiruvananthapuram, Kerala, India.
| | - Vafa Alakbarzade
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK. .,Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, London, UK.
| | - Mary Iype
- Department of Neurology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Royana Singh
- Department of Anatomy and Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
| | - Ajith Sreekantan-Nair
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK
| | - Barry A Chioza
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK.
| | - Tribhuvan M Mohapatra
- Department of Anatomy and Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
| | - Emma L Baple
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK. .,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK. .,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK.
| | - Michael A Patton
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK.,Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London, SW17 0RE, UK
| | - Thomas T Warner
- Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, London, UK
| | - Christos Proukakis
- Clinical Neuroscience, Royal Free Campus, UCL Institute of Neurology, London, UK.
| | - Abhi Kulkarni
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London, SW17 0RE, UK.
| | - Andrew H Crosby
- Molecular Genetics, RILD Institute, University of Exeter, Royal Devon and Exeter NHS Hospital, Wonford, Exeter, UK.
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15
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Cervantes A, García-Delgado C, Fernández-Ramírez F, Galaz-Montoya C, Morales-Jiménez AB, Nieto-Martínez K, Gómez-Laguna L, Villa-Morales J, Quintana-Palma M, Berúmen J, Kofman S, Morán-Barroso VF. Trisomy 1q41-qter and monosomy 3p26.3-pter in a family with a translocation (1;3): further delineation of the syndromes. BMC Med Genomics 2014; 7:55. [PMID: 25223409 PMCID: PMC4170088 DOI: 10.1186/1755-8794-7-55] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 09/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background Trisomy 1q and monosomy 3p deriving from a t(1;3) is an infrequent event. The clinical characteristics of trisomy 1q41-qter have been described but there is not a delineation of the syndrome. The 3p25.3-pter monosomy syndrome (MIM 613792) characteristics include low birth weight, microcephaly, psychomotor and growth retardation and abnormal facies. Case presentation A 2 years 8 months Mexican mestizo male patient was evaluated due to a trisomy 1q and monosomy 3p derived from a familial t(1;3)(q41;q26.3). Four female carriers of the balanced translocation and one relative that may have been similarly affected as the proband were identified. The implicated chromosomal regions were defined by microarray analysis, the patient had a trisomy 1q41-qter of 30.3 Mb in extension comprising about 240 protein coding genes and a monosomy 3p26.3-pter of 1.7 Mb including only the genes CNTN6 (MIM 607220) and CHL1 (MIM 607416), which have been implicated in dendrite development. Their contribution to the phenotype, regarding the definition of trisomy 1q41-qter and monosomy 3p26.3-pter syndromes are discussed. Conclusion We propose that a trisomy 1q41-qter syndrome should be considered in particular when the following characteristics are present: postnatal growth delay, macrocephaly, wide fontanelle, triangular facies, frontal bossing, thick eye brows, down slanting palpebral fissures, hypertelorism, flat nasal bridge, hypoplasic nostrils, long filtrum, high palate, microretrognathia, ear abnormalities, neural abnormalities (in particular ventricular dilatation), psychomotor developmental delay and mental retardation. Our patient showed most of these clinical characteristics with exception of macrocephaly, possibly due to a compensatory effect by haploinsufficiency of the two genes lost from 3p. The identification of carriers has important implications for genetic counseling as the risk of a new born with either a der(3) or der(1) resulting from an adjacent-1 segregation is of 25% for each of them, as the products of adjacent-2 or 3:1 segregations are not expected to be viable.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Verónica F Morán-Barroso
- Departamento de Genética, Hospital Infantil de México Federico Gómez, Calle Dr, Márquez 162, Col, Doctores, Del, Cuauhtémoc, 06720 México, D,F,, México.
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16
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Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. Eur J Hum Genet 2014; 23:753-60. [PMID: 25138099 DOI: 10.1038/ejhg.2014.165] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 01/02/2023] Open
Abstract
Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.
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17
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Moghadasi S, van Haeringen A, Langendonck L, Gijsbers ACJ, Ruivenkamp CAL. A terminal 3p26.3 deletion is not associated with dysmorphic features and intellectual disability in a four-generation family. Am J Med Genet A 2014; 164A:2863-8. [PMID: 25123480 DOI: 10.1002/ajmg.a.36700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/20/2014] [Indexed: 11/06/2022]
Abstract
Terminal deletions of the distal part of the short arm of chromosome 3 cause a wide range of phenotypes from normal to dysmorphic including microcephaly, developmental delay and intellectual disability. We studied the clinical consequences of a terminal deletion of the short arm of chromosome 3 in four generations of a family. The index patient is a14-month-old boy with microcephaly, corpus callosum dysgenesis, and minor dysmorphic features. Single Nucleotide Polymorphism (SNP) array analysis detected a duplication on the long arm of chromosome 6. His apparently healthy mother carries the same 6q duplication, but as an unexpected finding a terminal deletion of 2.9 Mb of the short arm of chromosome 3 was observed. Further co-segregation analysis in the family for the chromosome 3 deletion showed that with the exception of the sister of the index who has autism, speech delay, and learning problems, family members in four generations of this family are carrier of this 3p deletion and apparently healthy. To our knowledge, this is the first report of a study of this terminal 3p deletion in four generations. In this report, we review the literature on terminal 3p deletions and discuss the importance of molecular testing and reporting of copy number variants to achieve accurate genetic counseling in prenatal and postnatal screening.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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18
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Byeon JH, Shin E, Kim GH, Lee K, Hong YS, Lee JW, Eun BL. Application of array-based comparative genomic hybridization to pediatric neurologic diseases. Yonsei Med J 2014; 55:30-6. [PMID: 24339284 PMCID: PMC3874920 DOI: 10.3349/ymj.2014.55.1.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Array comparative genomic hybridization (array-CGH) is a technique used to analyze quantitative increase or decrease of chromosomes by competitive DNA hybridization of patients and controls. This study aimed to evaluate the benefits and yield of array-CGH in comparison with conventional karyotyping in pediatric neurology patients. MATERIALS AND METHODS We included 87 patients from the pediatric neurology clinic with at least one of the following features: developmental delay, mental retardation, dysmorphic face, or epilepsy. DNA extracted from patients and controls was hybridized on the Roche NimbleGen 135K oligonucleotide array and compared with G-band karyotyping. The results were analyzed with findings reported in recent publications and internet databases. RESULTS Chromosome imbalances, including 9 cases detected also by G-band karyotyping, were found in 28 patients (32.2%), and at least 19 of them seemed to be causally related to the abnormal phenotypes. Regarding each clinical symptom, 26.2% of 42 developmental delay patients, 44.4% of 18 mental retardation patients, 42.9% of 28 dysmorphic face patients, and 34.6% of 26 epilepsy patients showed abnormal array results. CONCLUSION Although there were relatively small number of tests in patients with pediatric neurologic disease, this study demonstrated that array-CGH is a very useful tool for clinical diagnosis of unknown genome abnormalities performed in pediatric neurology clinics.
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Affiliation(s)
- Jung Hye Byeon
- Department of Pediatrics, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 152-703, Korea.
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19
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Helbig I, Swinkels MEM, Aten E, Caliebe A, van 't Slot R, Boor R, von Spiczak S, Muhle H, Jähn JA, van Binsbergen E, van Nieuwenhuizen O, Jansen FE, Braun KPJ, de Haan GJ, Tommerup N, Stephani U, Hjalgrim H, Poot M, Lindhout D, Brilstra EH, Møller RS, Koeleman BPC. Structural genomic variation in childhood epilepsies with complex phenotypes. Eur J Hum Genet 2013; 22:896-901. [PMID: 24281369 DOI: 10.1038/ejhg.2013.262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 10/01/2013] [Accepted: 10/18/2013] [Indexed: 11/09/2022] Open
Abstract
A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies.
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Affiliation(s)
- Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Marielle E M Swinkels
- 1] Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands [2] SEIN Epilepsy Institute in the Netherlands Foundation, Hoofddorp, The Netherlands
| | - Emmelien Aten
- Department of Medical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Ruben van 't Slot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rainer Boor
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Sarah von Spiczak
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Ellen van Binsbergen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Onno van Nieuwenhuizen
- Department of Child Neurology, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, The Netherlands
| | - Floor E Jansen
- Department of Child Neurology, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, The Netherlands
| | - Kees P J Braun
- Department of Child Neurology, Rudolf Magnus Institute of Neurosciences, University Medical Center Utrecht, The Netherlands
| | - Gerrit-Jan de Haan
- SEIN Epilepsy Institute in the Netherlands Foundation, Hoofddorp, The Netherlands
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Copenhagen, Denmark
| | - Ulrich Stephani
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Helle Hjalgrim
- 1] Danish Epilepsy Centre, Dianalund, Denmark [2] Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- 1] Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands [2] SEIN Epilepsy Institute in the Netherlands Foundation, Hoofddorp, The Netherlands
| | - Eva H Brilstra
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rikke S Møller
- 1] Wilhelm Johannsen Centre for Functional Genome Research, Copenhagen, Denmark [2] Danish Epilepsy Centre, Dianalund, Denmark
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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20
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Eto K, Sakai N, Shimada S, Shioda M, Ishigaki K, Hamada Y, Shinpo M, Azuma J, Tominaga K, Shimojima K, Ozono K, Osawa M, Yamamoto T. Microdeletions of 3p21.31 characterized by developmental delay, distinctive features, elevated serum creatine kinase levels, and white matter involvement. Am J Med Genet A 2013; 161A:3049-56. [DOI: 10.1002/ajmg.a.36156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 06/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Kaoru Eto
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Norio Sakai
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Shino Shimada
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Mutsuki Shioda
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Keiko Ishigaki
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Yusuke Hamada
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Michiko Shinpo
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Junji Azuma
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Koji Tominaga
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Keiichi Ozono
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Makiko Osawa
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
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21
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Zhou J, McCarrey JR, Wang PJ. A 1.1-Mb segmental deletion on the X chromosome causes meiotic failure in male mice. Biol Reprod 2013; 88:159. [PMID: 23677977 DOI: 10.1095/biolreprod.112.106963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The mammalian X chromosome contains a large number of multicopy genes that are expressed during spermatogenesis. The roles of these genes during germ cell development and the functional significance of gene multiplication remain mostly unexplored, as the presence of multicopy gene families poses a challenge for genetic studies. Here we report the deletion of a 1.1-Mb segment of the mouse X chromosome that is syntenic with the human Xq22.1 region and contains 20 genes that are expressed predominantly in testis and brain, including three members of the nuclear export factor gene family (Nxf2, Nxf3, and Nxf7) and five copies of preferentially expressed antigen in melanoma-like 3 (Pramel3). We have shown that germline-specific Cre/loxP-mediated deletion of this 1.1-Mb segment is efficient and causes defective chromosomal synapsis, meiotic arrest, and sterility in male mice. Our results demonstrate that this 1.1-Mb region contains one or more novel X-linked factors that are essential for male meiosis.
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Affiliation(s)
- Jian Zhou
- Center for Animal Transgenesis and Germ Cell Research, Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
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22
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Li C, Mahajan V, Wang JC, Paes B. Monosomy 3pter-p25.3 and trisomy 1q42.13-qter in a boy with profound growth and developmental restriction, multiple congenital anomalies, and early death. Pediatr Neonatol 2013; 54:202-6. [PMID: 23597526 DOI: 10.1016/j.pedneo.2013.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 06/20/2012] [Accepted: 01/16/2013] [Indexed: 11/24/2022] Open
Abstract
Albeit rare, 3pter-p25 monosomy or 1q42-qter trisomy syndromes have been documented in the literature. Here, we report a unique case with a combination of 3pter-p25 monosomy and 1q42-qter trisomy, delineated by array comparative genomic hybridization analysis. The proband was a newborn male with multiple congenital anomalies that included brain malformation, ocular anomalies, trachea-laryngomalacia, cardiac defects, intestinal malrotation, and cutaneous findings in conjunction with biochemical anomalies, profound growth and developmental restriction, and early death. To our knowledge, this is the first case report of this unique chromosomal imbalance.
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Affiliation(s)
- Chumei Li
- Division of Clinical Genetics, McMaster University, Hamilton, Canada.
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23
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Poot M, Verrijn Stuart AA, van Daalen E, van Iperen A, van Binsbergen E, Hochstenbach R. Variable behavioural phenotypes of patients with monosomies of 15q26 and a review of 16 cases. Eur J Med Genet 2013; 56:346-50. [PMID: 23603061 DOI: 10.1016/j.ejmg.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 04/03/2013] [Indexed: 02/07/2023]
Abstract
Patients with trisomy or tetrasomy of distal 15q show a recognizable overgrowth syndrome, whereas patients with a monosomy of 15q26 share some degree of pre- and postnatal growth retardation, but differ with respect to facial and skeletal dysmorphisms, congenital heart disease and intellectual development. By reviewing 16 cases with losses of 15q26 we found that the size of the deletion was also not a predictor of the breadth of the phenotypic spectrum, the severity of disease or prognosis of the patient. Although monosomies of 15q26 do not represent a classical contiguous gene syndrome, a few candidate genes for selected features such as proportional growth retardation and cardiac abnormalities have been identified. In 11 out of 16 patients with monosomy of distal 15q variable neurobehavioral phenotypes, including learning difficulties, seizures, attention-deficit-hyperactivity disorder, hearing loss and autism, have been found. We discuss clinical ramifications for cases with a loss of 15q26 detected by prenatal array-CGH.
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Affiliation(s)
- Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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24
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A rare chromosome 3 imbalance and its clinical implications. Case Rep Pediatr 2012; 2012:846564. [PMID: 23097735 PMCID: PMC3477540 DOI: 10.1155/2012/846564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/09/2012] [Indexed: 11/18/2022] Open
Abstract
The duplication of chromosome 3q is a rare disorder with varying chromosomal breakpoints and consequently symptoms. Even rarer is the unbalanced outcome from a parental inv(3) resulting in duplicated 3q and a deletion of 3p. Molecular karyotyping should aid in precisely determining the length and breakpoints of the 3q+/3p− so as to better understand a child's future development and needs. We report a case of an infant male with a 57.5 Mb duplication from 3q23-qter. This patient also has an accompanying 1.7 Mb deletion of 3p26.3. The duplicated segment in this patient encompasses the known critical region of 3q26.3-q27, which is implicated in the previously reported 3q dup syndrome; however, the accompanying 3p26.3 deletion is smaller than the previously reported cases. The clinical phenotype of this patient relates to previously reported cases of 3q+ that may suggest that the accompanying 1.7 Mb heterozygous deletion is not clinically relevant. Taken together, our data has refined the location and extent of the chromosome 3 imbalance, which will aid in better understanding the molecular underpinning of the 3q syndrome.
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25
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dos Santos AP, Vieira TP, Simioni M, Monteiro FP, Gil-da-Silva-Lopes VL. Partial monosomy 21 (q11.2→q21.3) combined with 3p25.3→pter monosomy due to an unbalanced translocation in a patient presenting dysmorphic features and developmental delay. Gene 2012; 513:301-4. [PMID: 23031812 DOI: 10.1016/j.gene.2012.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/28/2012] [Accepted: 09/03/2012] [Indexed: 12/14/2022]
Abstract
We describe a female patient of 1 year and 5 months-old, referred for genetic evaluation due to neuropsychomotor delay, hearing impairment and dysmorphic features. The patient presents a partial chromosome 21 monosomy (q11.2→q21.3) in combination with a chromosome 3p terminal monosomy (p25.3→pter) due to an unbalanced de novo translocation. The translocation was confirmed by fluorescence in situ hybridization (FISH) and the breakpoints were mapped with high resolution array. After the combined analyses with these techniques the final karyotype was defined as 45,XX,der(3)t(3;21)(p25.3;q21.3)dn,-21.ish der(3)t(3;21)(RP11-329A2-,RP11-439F4-,RP11-95E11-,CTB-63H24+).arr 3p26.3p25.3(35,333-10,888,738))×1,21q11.2q21.3(13,354,643-27,357,765)×1. Analysis of microsatellite DNA markers pointed to a paternal origin for the chromosome rearrangement. This is the first case described with a partial proximal monosomy 21 combined with a 3p terminal monosomy due to a de novo unbalanced translocation.
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Affiliation(s)
- Ana Paula dos Santos
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, UNICAMP, Campinas, SP, Brazil
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26
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Riess A, Grasshoff U, Schäferhoff K, Bonin M, Riess O, Horber V, Tzschach A. Interstitial 3p25.3-p26.1 deletion in a patient with intellectual disability. Am J Med Genet A 2012; 158A:2587-90. [PMID: 22965684 DOI: 10.1002/ajmg.a.35562] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/21/2012] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of the short arm of chromosome 3 are rare. We report on a 3-year-old girl with intellectual disability, muscular hypotonia, strabismus, and facial anomalies in whom an interstitial 1.24 Mb deletion in 3p25.3-p26.1 was detected by SNP array analysis. The deleted region harbors 11 RefSeq genes including CAV3 and SRGAP3/MEGAP, which had been associated with muscle disorders and intellectual disability, respectively. The deletion overlaps with a slightly larger deletion in a girl with a more complex phenotype including congenital heart defect and epilepsy, which indicates that haploinsufficiency of one or several of the genes in the deleted interval causes intellectual deficits, but not heart defects or epilepsy. Thus, the patient broadens our knowledge of the phenotypic consequences of deletions in 3p25.3-p26.1 and facilitates genotype-phenotype correlations for chromosome aberrations of this region.
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Affiliation(s)
- Angelika Riess
- Institute of Human Genetics, University of Tuebingen, Germany
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27
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Peltekova IT, Macdonald A, Armour CM. Microdeletion on 3p25 in a patient with features of 3p deletion syndrome. Am J Med Genet A 2012; 158A:2583-6. [PMID: 22903836 DOI: 10.1002/ajmg.a.35559] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/17/2012] [Indexed: 11/10/2022]
Abstract
The rare 3p deletion syndrome presents with a spectrum of anomalies caused by deletions of variable lengths within the short arm of chromosome 3. While most of these deletions involve the 3p terminus, interstitial deletions may also give rise to features of the syndrome. We have detected an interstitial deletion of 643 kb in a patient who displayed many of the typical 3p deletion features. This patient had a number of findings in common with a previously reported patient, who had a 1.6 Mb interstitial deletion, including cognitive handicap, seizures, and congenital heart defects. A 518 kb region of overlap containing 12 genes may prove to be a critical region for some of these features. The putative functions of several genes, such as CRELD1, SRGAP3, CAMK1, TADA3, and MTMR14 are discussed with respect to their potential involvement in the 3p deletion syndrome phenotype. We suggest that this 518 kb area of overlap may define a critical region, which when deleted, can give rise to the 3p deletion syndrome phenotype.
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Affiliation(s)
- Iskra T Peltekova
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
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28
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Guilherme RS, Bragagnolo S, Pellegrino R, Christofolini DM, Takeno SS, Carvolheira GM, Kulikowski LD, Melaragno MI. Clinical, cytogenetic and molecular study in a case of r(3) with 3p deletion and review of the literature. Cytogenet Genome Res 2011; 134:325-30. [PMID: 21849783 DOI: 10.1159/000329478] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2011] [Indexed: 11/19/2022] Open
Abstract
Ring chromosome 3 is a rare abnormality with only 10 patients described in the literature. We report a patient with r(3) and ∼6-Mb distal 3p deletion. Single nucleotide polymorphism array, multiplex ligation-dependent probe amplification and fluorescence in situ hybridization techniques revealed that the ring was formed by a break in 3p26.1 and fusion with the subtelomeric region of 3q. The patient presents delayed psychomotor development, growth failure, minor anomalies and other features similar to patients with 3p monosomy. The analysis of 300 metaphase cells using G-banding and fluorescence in situ hybridization with centromeric probe revealed ring instability resulting in cells with secondary aberrations and with ring loss that could also be related to some phenotypic characteristics such as growth delay. This is the first patient with r(3) studied using molecular techniques that determined the exact breakpoints in order to establish a better karyotype-phenotype correlation.
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Affiliation(s)
- R Santos Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
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29
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Cuoco C, Ronchetto P, Gimelli S, Béna F, Divizia MT, Lerone M, Mirabelli-Badenier M, Mascaretti M, Gimelli G. Microarray based analysis of an inherited terminal 3p26.3 deletion, containing only the CHL1 gene, from a normal father to his two affected children. Orphanet J Rare Dis 2011; 6:12. [PMID: 21457564 PMCID: PMC3090742 DOI: 10.1186/1750-1172-6-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 04/01/2011] [Indexed: 11/27/2022] Open
Abstract
Background terminal deletions of the distal portion of the short arm of chromosome 3 cause a rare contiguous gene disorder characterized by growth retardation, developmental delay, mental retardation, dysmorphisms, microcephaly and ptosis. The phenotype of individuals with deletions varies from normal to severe. It was suggested that a 1,5 Mb minimal terminal deletion including the two genes CRBN and CNTN4 is sufficient to cause the syndrome. In addition the CHL1 gene, mapping at 3p26.3 distally to CRBN and CNTN4, was proposed as candidate gene for a non specific mental retardation because of its high level of expression in the brain. Methods and Results we describe two affected siblings in which array-CGH analysis disclosed an identical discontinuous terminal 3p26.3 deletion spanning less than 1 Mb. The deletion was transmitted from their normal father and included only the CHL1 gene. The two brothers present microcephaly, light mental retardation, learning and language difficulties but not the typical phenotype manifestations described in 3p- syndrome. Conclusion a terminal 3p26.3 deletion including only the CHL1 gene is a very rare finding previously reported only in one family. The phenotype of the affected individuals in the two families is very similar and the deletion has been inherited from an apparently normal parent. As already described for others recurrent syndromes with variable phenotype, these findings are challenging in genetic counselling because of an evident variable penetrance.
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Affiliation(s)
- Cristina Cuoco
- Laboratorio di Citogenetica, Istituto G. Gaslini, 16147 Genova, Italy
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30
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Gunnarsson C, Foyn Bruun C. Molecular characterization and clinical features of a patient with an interstitial deletion of 3p25.3-p26.1. Am J Med Genet A 2011; 152A:3110-4. [PMID: 21082655 DOI: 10.1002/ajmg.a.33353] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Distal chromosome 3p deletions (3p- syndrome) are associated with various developmental defects. The majority of cases have a terminal deletion of the short arm of chromosome 3 with loss of either the maternal or the paternal copy. A girl with an interstitial molecularly characterized 1.6 Mb deletion in cytoband 3p25.3-26.1 of the paternal chromosome 3 is presented. To our knowledge, she possesses the smallest deletion that has ever been reported for a patient with a clinical phenotype in accordance with the 3p- syndrome. The boundaries of the deletion lies within nearly all previously reported terminal deletions causing this syndrome. Selected genes that are present in the hemizygous state and which might be important for the phenotype of this patient as regards the congenital heart defect, autistic behavior and mental retardation (CAV3, OXTR, and SRGAP3/MEGAP, respectively) are discussed in context of the clinical features.
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Affiliation(s)
- Cecilia Gunnarsson
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, University Hospital, Linköping University, Linköping, Sweden.
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31
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Cottrell CE, Bir N, Varga E, Alvarez CE, Bouyain S, Zernzach R, Thrush DL, Evans J, Trimarchi M, Butter EM, Cunningham D, Gastier-Foster JM, McBride KL, Herman GE. Contactin 4 as an autism susceptibility locus. Autism Res 2011; 4:189-99. [PMID: 21308999 DOI: 10.1002/aur.184] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 12/15/2010] [Indexed: 01/05/2023]
Abstract
Structural and sequence variation have been described in several members of the contactin (CNTN) and contactin-associated protein (CNTNAP) gene families in association with neurodevelopmental disorders, including autism. Using array comparative genome hybridization (CGH), we identified a maternally inherited ∼535 kb deletion at 3p26.3 encompassing the 5' end of the contactin 4 gene (CNTN4) in a patient with autism. Based on this finding and previous reports implicating genomic rearrangements of CNTN4 in autism spectrum disorders (ASDs) and 3p- microdeletion syndrome, we undertook sequencing of the coding regions of the gene in a local ASD cohort in comparison with a set of controls. Unique missense variants were identified in 4 of 75 unrelated individuals with ASD, as well as in 1 of 107 controls. All of the amino acid substitutions were nonsynonomous, occurred at evolutionarily conserved positions, and were, thus, felt likely to be deleterious. However, these data did not reach statistical significance, nor did the variants segregate with disease within all of the ASD families. Finally, there was no detectable difference in binding of two of the variants to the interacting protein PTPRG in vitro. Thus, additional larger studies will be necessary to determine whether CNTN4 functions as an autism susceptibility locus in combination with other genetic and/or environmental factors.
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Affiliation(s)
- Catherine E Cottrell
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
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32
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Dundar M, Kiraz A, Tasdemir S, Akalin H, Kurtoglu S, Hafo F, Cine N, Savli H. Unbalanced 3;22 translocation with 22q11 and 3p deletion syndrome. Am J Med Genet A 2011; 152A:2791-5. [PMID: 20949503 DOI: 10.1002/ajmg.a.33249] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This report describes a 25-day-old Turkish boy with unbalanced 3;22 translocation that includes the 22q11.2 deletion and 3p25 deletion syndrome. The karyotype was 45, XY,der(3)t(3;22)(p25;q11),-22. Although no immunological dysfunction could be demonstrated, the boy presented some manifestations of DiGeorge anomaly (DGA), which has been associated with monosomy for the same region of chromosome 22, velocardiofacial syndrome (VCFS), and the 3p deletion syndrome. Clinical features include short stature, hypertelorism, low set ears, cleft lip with cleft palate, short neck, truncus arteriosus, micropenis, clubfoot, over riding toes on right foot, four digits on left foot and growth delay. In addition he had feeding difficulties, respiratory infections, and developmental delay. Fluorescence in situ hybridization (FISH) studies confirmed loss of the proximal DiGeorge chromosomal region (DGCR). Array CGH analysis showed the deletion sites on chromosomes 3 and 22. This report documents a rare chromosomal aberration that causes the 22q11 and 3p deletion syndrome simultaneously.
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Affiliation(s)
- Munis Dundar
- Department of Medical Genetics, Erciyes University Medical Faculty, Kayseri, Turkey.
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33
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Rajaei S, Erlandson A, Kyllerman M, Albage M, Lundstrom I, Karrstedt EL, Hagberg B. Early infantile onset ''congenital'' Rett syndrome variants: Swedish experience through four decades and mutation analysis. J Child Neurol 2011; 26:65-71. [PMID: 21212452 DOI: 10.1177/0883073810374125] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The early infantile onset ''congenital'' variant of Rett syndrome presents with deviations of behavior from very early infancy. Here, we report on a clinical-genetic study in a collected series of 14 Swedish girls with early infantile onset Rett syndrome phenotype. The clinical diagnosis was based on symptom onset before the age of 6 months and the patients fulfilled 3 or more Rett variant criteria and 5 or more supportive criteria. Genotype-phenotype correlation studies in the CDKL5-gene have recently shown clinical associations to early infantile onset Rett variants. Mutation analyses for both the MECP2-gene and the CDKL5-gene were, therefore, performed. Of interest, we found a large deletion covering 2 exons in MECP2, which underlines the importance of MECP2 mutation screening even for the ''atypical'' early infantile onset variants of Rett syndrome. No early infantile onset Rett syndrome patients in this study had the previously well-known hotspot mutations in the MECP2-gene.
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Affiliation(s)
- Saideh Rajaei
- Department of Medical and Clinical Genetics, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
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34
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Lindstrand A, Malmgren H, Verri A, Benetti E, Eriksson M, Nordgren A, Anderlid BM, Golovleva I, Schoumans J, Blennow E. Molecular and clinical characterization of patients with overlapping 10p deletions. Am J Med Genet A 2010; 152A:1233-43. [DOI: 10.1002/ajmg.a.33366] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Lindstrand A, Schoumans J, Gustavsson P, Hanemaaijer N, Malmgren H, Blennow E. Improved structural characterization of chromosomal breakpoints using high resolution custom array-CGH. Clin Genet 2010; 77:552-62. [DOI: 10.1111/j.1399-0004.2009.01341.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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36
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Pohjola P, de Leeuw N, Penttinen M, Kääriäinen H. Terminal 3p deletions in two families-Correlation between molecular karyotype and phenotype. Am J Med Genet A 2010; 152A:441-6. [DOI: 10.1002/ajmg.a.33215] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Shuib S, McMullan D, Rattenberry E, Barber RM, Rahman F, Zatyka M, Chapman C, Macdonald F, Latif F, Davison V, Maher ER. Microarray based analysis of 3p25-p26 deletions (3p- syndrome). Am J Med Genet A 2009; 149A:2099-105. [PMID: 19760623 DOI: 10.1002/ajmg.a.32824] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Distal deletion of chromosome 3p25-pter (3p- syndrome) produces a distinct clinical syndrome characterized by low birth weight, mental retardation, telecanthus, ptosis, and micrognathia. Congenital heart disease (CHD), typically atrioventricular septal defect (AVSD) occurs in about a third of patients. Previously we reported on an association between the presence of CHD and the proximal extent of the deletion such that a CHD susceptibility gene was mapped between D3S1263 and D3S3594. In addition, we and others have suggested several candidate genes for the psychomotor retardation usually seen with constitutional 3p25 deletions. In order to further investigate genotype-phenotype correlations in 3p- syndrome we analyzed 14 patients with cytogenetically detectable deletions of 3p25 (including one patient with a normal phenotype) using Affymetrix 250K SNP microarrays. Deletion size varied from approximately 6 to 12 Mb. Assuming complete penetrance, a candidate critical region for a CHD susceptibility gene was refined to approximately 200 kb and a candidate critical region for mental retardation was mapped to an approximately 1 Mb interval containing SRGAP3 but other 3p neurodevelopmental genes including CHL1, CNTN4, LRRN1, and ITPR1 mapped outside the candidate critical interval. We suggest that current evidence suggests that SRGAP3 is the major determinant of mental retardation in distal 3p deletions.
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Affiliation(s)
- Salwati Shuib
- Department of Medical and Molecular Genetics, University of Birmingham, Birmingham, UK
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38
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Brancati F, Bernardini L, Cavalcanti DP, Romano C, Novelli A, Dallapiccola B. Genome rearrangements in patients with blepharophimosis, mental retardation and hypothyroidism, so-called Young-Simpson syndrome. Clin Genet 2009; 76:210-3. [PMID: 19659891 DOI: 10.1111/j.1399-0004.2009.01235.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Van den Veyver IB, Patel A, Shaw CA, Pursley AN, Kang SHL, Simovich MJ, Ward PA, Darilek S, Johnson A, Neill SE, Bi W, White LD, Eng CM, Lupski JR, Cheung SW, Beaudet AL. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenat Diagn 2009; 29:29-39. [PMID: 19012303 DOI: 10.1002/pd.2127] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To evaluate the use of array comparative genomic hybridization (aCGH) for prenatal diagnosis, including assessment of variants of uncertain significance, and the ability to detect abnormalities not detected by karyotype, and vice versa. METHODS Women undergoing amniocentesis or chorionic villus sampling (CVS) for karyotype were offered aCGH analysis using a targeted microarray. Parental samples were obtained concurrently to exclude maternal cell contamination and determine if copy number variants (CNVs) were de novo, or inherited prior to issuing a report. RESULTS We analyzed 300 samples, most were amniotic fluid (82%) and CVS (17%). The most common indications were advanced maternal age (N=123) and abnormal ultrasound findings (N=84). We detected 58 CNVs (19.3%). Of these, 40 (13.3%) were interpreted as likely benign, 15 (5.0%) were of defined pathological significance, while 3 (1.0%) were of uncertain clinical significance. For seven (approximately 2.3% or 1/43), aCGH contributed important new information. For two of these (1% or approximately 1/150), the abnormality would not have been detected without aCGH analysis. CONCLUSION Although aCGH-detected benign inherited variants in 13.3% of cases, these did not present major counseling difficulties, and the procedure is an improved diagnostic tool for prenatal detection of chromosomal abnormalities.
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40
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Nucaro AL, Meloni M, Pisano T, Melis P, Rossi E, Rossino R, Corona S, Loi M, Achena F, Zuffardi O, Cianchetti C. Familial translocation t(3;10) (p26.3;p12.31) leading to trisomy 10p12.31-->pter and monosomy 3p26.3-->pter in seven members. Am J Med Genet A 2008; 146A:3242-5. [PMID: 19012344 DOI: 10.1002/ajmg.a.32590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Lisa Nucaro
- Institute of Neurogenetic and Neuropharmacology of CNR, Monserrato, Cagliari, Italy.
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41
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Fernandez TV, García-González I, Mason CE, Hernández-Zaragoza G, Ledezma-Rodríguez V, Anguiano-Alvarez V, E'Vega R, Gutiérrez-Angulo M, Maya M, García-Bejarano H, González-Cruz M, Barrios S, Atorga R, López-Cardona M, Armendariz-Borunda J, State MW, Dávalos NO. Molecular characterization of a patient with 3p deletion syndrome and a review of the literature. Am J Med Genet A 2008; 146A:2746-52. [DOI: 10.1002/ajmg.a.32533] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Gijsbers ACJ, D'haene B, Hilhorst-Hofstee Y, Mannens M, Albrecht B, Seidel J, Witt DR, Maisenbacher MK, Loeys B, van Essen T, Bakker E, Hennekam R, Breuning MH, De Baere E, Ruivenkamp CAL. Identification of copy number variants associated with BPES-like phenotypes. Hum Genet 2008; 124:489-98. [PMID: 18953567 DOI: 10.1007/s00439-008-0574-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 10/10/2008] [Indexed: 11/24/2022]
Abstract
Blepharophimosis-Ptosis-Epicanthus inversus syndrome (BPES) is a well-characterized rare syndrome that includes an eyelid malformation associated with (type I) or without premature ovarian failure (type II). Patients with typical BPES have four major characteristics: blepharophimosis, ptosis, epicanthus inversus and telecanthus. Mutations in the FOXL2 gene, encoding a forkhead transcription factor, are responsible for the majority of both types of BPES. However, many patients with BPES-like features, i.e., having at least two major characteristics of BPES, have an unidentified cause. Here, we report on a group of 27 patients with BPES-like features, but without an identified genetic defect in the FOXL2 gene or flanking region. These patients were analyzed with whole-genome high-density arrays in order to identify copy number variants (CNVs) that might explain the BPES-like phenotype. In nine out of 27 patients (33%) CNVs not previously described as polymorphisms were detected. Four of these patients displayed psychomotor retardation as an additional clinical characteristic. In conclusion, we demonstrate that BPES-like phenotypes are frequently caused by CNVs, and we emphasize the importance of whole-genome copy number screening to identify the underlying genetic causes of these phenotypes.
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Affiliation(s)
- Antoinet C J Gijsbers
- Center for Human and Clinical Genetics, Leiden University Medical Center, Postzone S-6-P, Einthovenweg 20, 2333 CZ, Leiden, The Netherlands.
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Barber JCK. Terminal 3p deletions: phenotypic variability, chromosomal non-penetrance, or gene modification? Am J Med Genet A 2008; 146A:1899-901. [PMID: 18553547 DOI: 10.1002/ajmg.a.32387] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hoo JJ, Shrimpton AE. Distal 3p deletion is not necessarily associated with dysmorphic features or psychomotor delay. Am J Med Genet A 2008; 146A:538. [DOI: 10.1002/ajmg.a.32158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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