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Hajek CA, Ji J, Saitta SC. Interstitial Chromosome 3p13p14 Deletions: An Update and Review. Mol Syndromol 2018; 9:122-133. [PMID: 29928177 DOI: 10.1159/000488168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2017] [Indexed: 01/24/2023] Open
Abstract
Deletions of proximal chromosome 3p13p14 are infrequent chromosomal alterations. Variable sizes and breakpoints have been reported in patients with a wide range of phenotypes that are evolving as additional cases are reported. The routine use of high-density chromosomal microarrays (CMA) has allowed the identification of many more cases of this disorder and clinical phenotyping shows evidence for an emerging profile among patients with overlapping deletions of 3p13p14. Here, we review the currently reported cases, their phenotypes and where available, the genomic intervals delineated by CMA. Surprisingly, we found that a significant number of proximal chromosome 3p deletions involve structural rearrangements, especially insertions, that have been identified in balanced parental chromosome complements. This region is historically known as a common human chromosomal fragile site, although an underlying genomic mechanism related to its architecture has not been identified. We conclude that identification of an interstitial 3p deletion in a proband by CMA should prompt consideration of further structural chromosomal evaluation using more traditional cytogenetic techniques. While the variability in breakpoints does not suggest a unifying underlying mechanism for these alterations, identification of the haploinsufficient genes in each patient's deletion interval and their developmental roles can guide genotype-phenotype correlations and impact clinical management.
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Affiliation(s)
- Catherine A Hajek
- Sanford Health, and Department of Internal Medicine, University of South Dakota Sanford School of Medicine, Sioux Falls, SD
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles.,Department of Pathology, Keck USC School of Medicine, Los Angeles, CA, USA
| | - Sulagna C Saitta
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles.,Department of Pathology, Keck USC School of Medicine, Los Angeles, CA, USA
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2
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Dimitrov BI, Ogilvie C, Wieczorek D, Wakeling E, Sikkema-Raddatz B, van Ravenswaaij-Arts CMA, Josifova D. 3p14 deletion is a rare contiguous gene syndrome: report of 2 new patients and an overview of 14 patients. Am J Med Genet A 2015; 167:1223-30. [PMID: 25908055 DOI: 10.1002/ajmg.a.36556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/13/2014] [Indexed: 01/13/2023]
Abstract
Interstitial deletions of chromosome 3p14p12 are a rare chromosome rearrangement. Twenty-six patients have been reported in the literature to date, however, a specific clinical phenotype has not yet been delineated. We describe three patients (two new) with overlapping chromosome 3p14p12 deletions and review the clinical and molecular data of 11 well-characterized, published cases. These patients had a number of features in common, such as short stature, failure to thrive, facial dysmorphism, congenital heart defects, urogenital abnormalities, neurological problems, hearing loss, and global developmental delay, suggesting that the interstitial chromosome 3p14p12 deletion gives rise to a multiple congenital anomaly syndrome. Some of the patients show clinical overlap with other complex syndromes such as CHARGE syndrome. Genotype-phenotype analysis revealed candidate genes for parts of the clinical features suggesting that the 3p14 deletion is a contiguous gene syndrome.
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Affiliation(s)
- B I Dimitrov
- Department of Clinical Genetics, Guy's Hospital, London, United Kingdom
| | - C Ogilvie
- Genetics Laboratories, Guy's Hospital, London, United Kingdom
| | - D Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - E Wakeling
- North West Thames Regional Genetic Service, North West London Hospitals, NHS Trust, London, United Kingdom
| | - B Sikkema-Raddatz
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - C M A van Ravenswaaij-Arts
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - D Josifova
- Department of Clinical Genetics, Guy's Hospital, London, United Kingdom
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Thevenon J, Monnier N, Callier P, Dieterich K, Francoise M, Montgomery T, Kjaergaard S, Neas K, Dixon J, Dahm TL, Huet F, Ragon C, Mosca-Boidron AL, Marle N, Duplomb L, Aubriot-Lorton MH, Mugneret F, Vokes SA, Tucker HW, Lunardi J, Faivre L, Jouk PS, Thauvin-Robinet C. Delineation of the 3p14.1p13 microdeletion associated with syndromic distal limb contractures. Am J Med Genet A 2014; 164A:3027-34. [PMID: 25258245 DOI: 10.1002/ajmg.a.36751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/14/2014] [Indexed: 12/19/2022]
Abstract
Distal limb contractures (DLC) represent a heterogeneous clinical and genetic condition. Overall, 20-25% of the DLC are caused by mutations in genes encoding the muscle contractile apparatus. Large interstitial deletions of the 3p have already been diagnosed by standard chromosomal analysis, but not associated with a specific phenotype. We report on four patients with syndromic DLC presenting with a de novo 3p14.1p13 microdeletion. The clinical features associated multiple contractures, feeding problems, developmental delay, and intellectual disability. Facial dysmorphism was constant with low-set posteriorly rotated ears and blepharophimosis. Review of previously reported cases with a precise mapping of the deletions, documented a 250 kb smallest region of overlap (SRO) necessary for DLC. This region contained one gene, EIF4E3, the first three exons of the FOXP1 gene, and an intronic enhancer of FOXP1 named hs1149. Sanger sequencing and locus quantification of hs1149, EIF4E3, and FOXP1 in a cohort of 11 French patients affected by DLC appeared normal. In conclusion, we delineate a new microdeletion syndrome involving the 3p14.1p13 locus and associated with DLC and severe developmental delay.
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Affiliation(s)
- Julien Thevenon
- Fédération Hospitalo-Universitaire TRANSLAD et Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs» du Grand Est, Hôpital d'Enfants, CHU Dijon, Dijon, France; Université de Bourgogne, Dijon, France
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Ţuţulan-Cunită AC, Papuc SM, Arghir A, Rötzer KM, Deshpande C, Lungeanu A, Budişteanu M. 3p interstitial deletion: novel case report and review. J Child Neurol 2012; 27:1062-6. [PMID: 22290856 DOI: 10.1177/0883073811431016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
3p interstitial deletions have emerged in recent years as a new cause of neurodevelopmental delay and intellectual disability. Since the first report of this condition in 1979, 16 cases have been described in the literature, delineating it as a presumptive syndrome. Here, we add a novel case presenting severely delayed neurodevelopment and psychomotor development; facial dysmorphism (square facies, broad forehead, short palpebral fissures, epicanthic folds, broad nasal bridge, and low-set malformed ears); cerebral, cardiac, and genital malformations; hand and feet anomalies; sacral sinus; and hearing impairment. Genetic investigations revealed a del(3)(p12.3p14.1) of 12.5 Mb, including 31 ORFs, among which ROBO2, PDZRN3, MITF, and FOXP1 are known to act in neurodevelopment. The clinical features of our patient are compared with those previously reported in the literature, thus providing further support for the delineation of the 3p interstitial deletion syndrome.
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Pariani MJ, Spencer A, Graham JM, Rimoin DL. A 785kb deletion of 3p14.1p13, including the FOXP1 gene, associated with speech delay, contractures, hypertonia and blepharophimosis. Eur J Med Genet 2009; 52:123-7. [PMID: 19332160 PMCID: PMC2853231 DOI: 10.1016/j.ejmg.2009.03.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 03/12/2009] [Indexed: 01/08/2023]
Abstract
We report a child with a 785kb deletion of the 3p14.1p13 region including the genes FOXP1, EIF4E3, PROK2, GPR27 resulting in speech delay, contractures, hypertonia and blepharophimosis. FOXP1 and FOXP2 are transcription factors containing a polyglutamine tract and a forkhead DNA binding domain. They both play a role in the developing human foregut and brain [W. Shu, M.M. Lu, Y. Zhang, P. Tucker, D. Zhou, E.E. Morrisey, Foxp2 and Foxp1 cooperatively regulate lung and esophagus development, Development 134 (2007) 1991-2000, E. Spiteri, G. Konopka, G. Coppola, J. Bomar, M. Oldham, J. Ou, et al. Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain, Am. J. Hum. Genet. 81 (2007) 1144-1157, S. Tamura, Y. Morikawa, H. Iwanishi, T. Hisaoka, E. Senba. Expression pattern of the winged-helix/forkhead transcription factor Foxp1 in the developing central nervous system, Gene Expr. Patterns. 3 (2003) 193-197.]. Mutations in FOXP2 are known to cause severe speech and language abnormalities [C.S.L. Lai, S.E. Fisher, J.A. Hurst, F. Vargha-Khadem, A.P. Monaco, A forkhead-domain gene is mutated in a severe speech and language disorder, Nature 413 (2001) 519-523.] in humans and animals. It has been suggested that overlap of FOXP1 and FOXP2 expression in the songbird and human brain may indicate that mutations in FOXP1 would also result in speech and language abnormalities. The roles of EIF4E3, PROK2 and GPR27 are also evaluated.
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Affiliation(s)
- Mitchel J Pariani
- Medical Genetics Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA.
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Lalli C, Galasso C, Lo Castro A, Nardone AM, Di Paolo A, Curatolo P. Interstitial deletion of a proximal 3p: a clinically recognisable syndrome. Brain Dev 2007; 29:312-6. [PMID: 17125947 DOI: 10.1016/j.braindev.2006.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Revised: 09/22/2006] [Accepted: 09/27/2006] [Indexed: 11/26/2022]
Abstract
Interstitial deletions of the proximal short arm of chromosome 3 occurring as constitutional aberrations are rare and a defined clinical phenotype is not established yet. We report on a 30-months-old girl with distinct facial features (square facies, plagiocephaly, broad forehead, broad nasal bridge, long philtrum and low set ears) and psychomotor/speech delay associated with an interstitial deletion of 3p12 chromosomal band, del(3)(p12p12). Clinical manifestations of our child were compared with those of other eight patients with the same deletion previously described to further delineate the proximal 3p deletion syndrome.
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Affiliation(s)
- Cristina Lalli
- Neuroscience Department, Pediatric Neurology Unit, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
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Schwarzbraun T, Ofner L, Gillessen-Kaesbach G, Schaperdoth B, Preisegger KH, Windpassinger C, Wagner K, Petek E, Kroisel PM. A new 3p interstitial deletion including the entireMITF gene causes a variation of Tietz/Waardenburg type IIA syndromes. Am J Med Genet A 2007; 143A:619-24. [PMID: 17318840 DOI: 10.1002/ajmg.a.31627] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thomas Schwarzbraun
- Institute of Medical Biology and Human Genetics, Medical University of Graz, Graz, Austria
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Petek E, Windpassinger C, Simma B, Mueller T, Wagner K, Kroisel PM. Molecular characterisation of a 15 Mb constitutional de novo interstitial deletion of chromosome 3p in a boy with developmental delay and congenital anomalies. J Hum Genet 2004; 48:283-287. [PMID: 12836054 DOI: 10.1007/s10038-003-0023-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2003] [Accepted: 03/11/2003] [Indexed: 11/29/2022]
Abstract
We describe the case of a 22-month-old boy with developmental and psychomotor retardation as well as craniofacial dysmorphism, including a cleft lip. Analysis of G-banded chromosomes of the propositus showed a de novo interstitial deletion of the short arm of chromosome 3, del(3)(p13p11). Fine mapping of the deletion was performed using fluorescence in situ hybridisation analysis with region-specific BAC clones. Eight BACs were absent from one chromosome 3 from the patient. Molecular analyses of eleven polymorphic DNA markers helped to narrow down the breakpoints and demonstrated that the derivative chromosome 3 is of paternal origin. The deleted segment encompasses about 15 Mb between marker D3S3551 and the centromere. Only a small number of known genes, including PROK2, GPR27, RYBP, PPP4R2, ROBO1, and GBE1, which map in the 3p13-p11 region are included in the deletion.
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Affiliation(s)
- Erwin Petek
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, Harrachgasse 21/8, A-8010 , Graz, Austria.
| | - Christian Windpassinger
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, Harrachgasse 21/8, A-8010 , Graz, Austria
| | - Burkhard Simma
- Department of Pediatrics, Academic Teaching Hospital, Feldkirch, Austria
| | - Thomas Mueller
- Department of Pediatrics, Academic Teaching Hospital, Feldkirch, Austria
| | - Klaus Wagner
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, Harrachgasse 21/8, A-8010 , Graz, Austria
| | - Peter M Kroisel
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, Harrachgasse 21/8, A-8010 , Graz, Austria
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Wieczorek D, Bolt J, Schwechheimer K, Gillessen-Kaesbach G. A patient with interstitial deletion of the short arm of chromosome 3 (pter-->p21.2::p12-->qter) and a CHARGE-like phenotype. AMERICAN JOURNAL OF MEDICAL GENETICS 1997; 69:413-7. [PMID: 9098493 DOI: 10.1002/(sici)1096-8628(19970414)69:4<413::aid-ajmg15>3.0.co;2-q] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report on a 4-month-old boy with a de novo interstitial deletion of the short arm of chromosome 3 (pter-->p21.2::p12-->qter) and clinical findings typical of proximal 3p deletion together with coloboma of iris, heart defect, choanal atresia, retardation of growth and development, genital hypoplasia, and ear anomalies. Family history was unremarkable and parental chromosomes were normal. The clinical manifestations of the patient are compared with those of 10 patients previously described with a proximal 3p deletion. The additional CHARGE-like phenotype is discussed.
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Affiliation(s)
- D Wieczorek
- Institut für Humangenetik, Universitätklinikum Essen, Germany
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