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Luo M, Gu X, Zhou T, Chen C. Prenatal diagnosis and molecular cytogenetic analyses of a paternal inherited deletion of 1q23.3 encompassing PBX1 gene. Mol Cytogenet 2022; 15:53. [PMID: 36544198 PMCID: PMC9768991 DOI: 10.1186/s13039-022-00632-y] [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: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Patients with deletions involving the long arm of chromosome 1 are rare. The PBX1 gene is located on chromosome 1q23.3. PBX1 encodes a transcription factor which promotes protein-protein interaction and plays a crucial role in several developmental processes. PBX1 haploinsufficiency had been reported to lead syndromic congenital anomalies of kidney and urinary tract (CAKUT) in humans. CASE PRESENTATION In this research, a 24-year-old woman (gravida 1, para 0) underwent amniocentesis at 22 weeks' gestation because of a horseshoe kidney of the fetus on prenatal ultrasound. RESULTS Chromosomal microarray analysis (CMA) from this family revealed a 1.14 Mb paternal inherited deletion on chromosome 1q23.3, spanning from position 163,620,000 to 164,760,000 (hg19). Trio whole-exome sequencing (WES) showed heterozygous deletions in exons 1-2 of the PBX1 in fetal and paternal samples. At the 3-year follow-up, the baby did not have an abnormal phenotype except a horseshoe kidney. CONCLUSION We provide a detailed description of the phenotype in a family with paternal inherited deletion of 1q23.3 encompassing exons 1-2 of the PBX1 gene. Combination of karyotype analysis, CMA, WES, prenatal ultrasound and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.
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Affiliation(s)
- Man Luo
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Xia Gu
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Ting Zhou
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Chaoli Chen
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China.
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Petzold F, Jin W, Hantmann E, Korbach K, Schönauer R, Halbritter J. Novel somatic PBX1 mosaicism likely masking syndromic CAKUT in an adult with bilateral kidney hypoplasia. Clin Kidney J 2022; 15:1333-1339. [PMID: 35756743 PMCID: PMC9217644 DOI: 10.1093/ckj/sfac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Background Congenital abnormalities of the kidney and urinary tract (CAKUT) are characterized by vast phenotypic heterogeneity and incomplete penetrance. Although CAKUT represent the main cause of pediatric chronic kidney disease, only ∼20% can be explained by single-gene disorders to date. While pathogenic alterations of PBX1 were recently associated with a severe form of syndromic CAKUT, most CAKUT patients survive childhood and adolescence to reach end-stage kidney disease later in life. Although somatic mosaicism is known to attenuate severity in other kidney diseases, it has rarely been described or systematically been assessed in CAKUT. Methods We conducted an in-depth phenotypic characterization of the index patient and his family using targeted next-generation sequencing, segregation analysis and workup of mosaicism with DNA isolated from peripheral blood cells, oral mucosa and cultured urinary renal epithelial cells (URECs). Results Somatic mosaicism was identified in a 20-year-old male with sporadic but mild syndromic renal hypoplasia. He was found to carry a novel de novo truncating variant in PBX1 [c.992C>A, p.(Ser331*)]. This variant was detected in 26% of sequencing reads from blood cells, 50% from oral mucosa and 20% from cultured URECs. Conclusions PBX1-associated CAKUT is characterized by a wealth of de novo mutations. As in de novo cases, mutations can occur intra- or post-zygotically and genetic mosaicism might represent a more common phenomenon in PBX1 disease, accounting for variable expressivity on a general basis. Consequently we suggest ruling out somatic mosaicism in sporadic CAKUT, notably in attenuated and atypical clinical courses.
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Affiliation(s)
- Friederike Petzold
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Wenjun Jin
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Elena Hantmann
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Ria Schönauer
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan Halbritter
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Safgren SL, Olson RJ, Pinto E Vairo F, Bothun ED, Hanna C, Klee EW, Schimmenti LA. De novo PBX1 variant in a patient with glaucoma, kidney anomalies, and developmental delay: An expansion of the CAKUTHED phenotype. Am J Med Genet A 2022; 188:919-925. [PMID: 34797033 DOI: 10.1002/ajmg.a.62576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
An infant was referred for evaluation of congenital glaucoma and corneal clouding. In addition, he had a pelvic kidney, hypotonia, patent ductus arteriosus, abnormal pinnae, and developmental delay. Exome sequencing identified a previously unpublished de novo single nucleotide insertion in PBX1 c.400dupG (NM_002585.3), predicted to cause a frameshift resulting in a truncated protein with loss of function (p.Ala134Glyfs*65). Identification of this loss of function variant supports the diagnosis of congenital anomalies of the kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay (CAKUTHED). Here, we propose glaucoma as an extra-renal manifestation associated with PBX1-related disease due to the relationship of PBX1 with MEIS1, MEIS2, and FOXC1 transcription factors associated with eye development.
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Affiliation(s)
- Stephanie L Safgren
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rory J Olson
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Filippo Pinto E Vairo
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Erick D Bothun
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christian Hanna
- Department of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, USA
- Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Otorhinolaryngology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
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Song J, Zhang Q, Lu B, Gou Z, Wang T, Tang H, Xiang J, Jiang W, Deng X. Case Report: Candidate Genes Associated With Prenatal Ultrasound Anomalies in a Fetus With Prenatally Detected 1q23.3q31.2 Deletion. Front Genet 2021; 12:696624. [PMID: 34630509 PMCID: PMC8496901 DOI: 10.3389/fgene.2021.696624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Patients with deletions involving the long arm of chromosome 1 are rare, and the main aim of this study was to refine the genotype-phenotype correlation. Case Report: In this report, a 28-year-old pregnant woman, gravida 2 para 1, at 25+4 weeks of gestation underwent ultrasound examination in our institute. The ultrasonographic findings of the fetus were as follows: (1) fetal growth restriction; (2) cleft lip and palate; (3) bilateral renal hypoplasia; (4) lateral ventriculomegaly; (5) single umbilical artery; (6) absent stomach; (7) coronary sinus dilatation with persistent left superior vena cava, ventricular septal defect and unroofed coronary sinus syndrome. Chromosomal microarray analysis of amniotic fluid from the fetus revealed a 28.025 Mb deletion in 1q23.3q31.2, spanning from position 164,559,675 to 192,584,768 (hg19). Conclusion: Genotype-phenotype correlation might improve prenatal diagnosis of fetuses with chromosome 1q deletion. PBX1 could be a candidate gene for fetal growth restriction, renal hypoplasia and congenital heart disease. Fetal growth restriction was accompanied by decreased renal volume in the fetus. Combined with ultrasonic examination, the application of chromosomal microarray analysis will provide accurate prenatal diagnosis.
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Affiliation(s)
- Jiahao Song
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qian Zhang
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Bing Lu
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zhongshan Gou
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Hui Tang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Wei Jiang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xuedong Deng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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Fitzgerald KK, Powell-Hamilton N, Shillingford AJ, Robinson B, Gripp KW. Inherited intragenic PBX1 deletion: Expanding the phenotype. Am J Med Genet A 2021; 185:234-237. [PMID: 33098248 DOI: 10.1002/ajmg.a.61932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/10/2022]
Abstract
PBX1 encodes the pre-B cell leukemia homeobox transcription factor, a three amino acid loop extension (TALE) homeodomain transcription factor, which forms nuclear complexes with other TALE class homeodomain proteins that ultimately regulate target genes controlling organ patterning during embryogenesis. Heterozygous de novo pathogenic variants in PBX1 resulting in haploinsufficiency are associated with congenital anomalies of the kidneys and urinary tract, most commonly renal hypoplasia, as well as anomalies involving the external ear, branchial arch, heart, and genitalia, and they cause intellectual disability and developmental delay. Affected individuals described thus far have had de novo variants. Here, we report three related individuals with an inherited pathogenic intragenic PBX1 deletion with variable clinical features typical for this syndrome.
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Affiliation(s)
- Kristi K Fitzgerald
- Nemours Cardiac Center, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Nina Powell-Hamilton
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Amanda J Shillingford
- Nemours Cardiac Center, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Bradley Robinson
- Nemours Cardiac Center, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
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Arts P, Garland J, Byrne AB, Hardy TS, Babic M, Feng J, Wang P, Ha T, King‐Smith SL, Schreiber AW, Crawford A, Manton N, Moore L, Barnett CP, Scott HS. Paternal mosaicism for a novel PBX1 mutation associated with recurrent perinatal death: Phenotypic expansion of the PBX1-related syndrome. Am J Med Genet A 2020; 182:1273-1277. [PMID: 32141698 PMCID: PMC7217179 DOI: 10.1002/ajmg.a.61541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/09/2020] [Accepted: 02/13/2020] [Indexed: 11/11/2022]
Abstract
Autosomal dominant (de novo) mutations in PBX1 are known to cause congenital abnormalities of the kidney and urinary tract (CAKUT), with or without extra-renal abnormalities. Using trio exome sequencing, we identified a PBX1 p.(Arg107Trp) mutation in a deceased one-day-old neonate presenting with CAKUT, asplenia, and severe bilateral diaphragmatic thinning and eventration. Further investigation by droplet digital PCR revealed that the mutation had occurred post-zygotically in the father, with different variant allele frequencies of the mosaic PBX1 mutation in blood (10%) and sperm (20%). Interestingly, the father had subclinical hydronephrosis in childhood. With an expected recurrence risk of one in five, chorionic villus sampling and prenatal diagnosis for the PBX1 mutation identified recurrence in a subsequent pregnancy. The family opted to continue the pregnancy and the second affected sibling was stillborn at 35 weeks, presenting with similar severe bilateral diaphragmatic eventration, microsplenia, and complete sex reversal (46, XY female). This study highlights the importance of follow-up studies for presumed de novo and low-level mosaic variants and broadens the phenotypic spectrum of developmental abnormalities caused by PBX1 mutations.
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Affiliation(s)
- Peer Arts
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Jessica Garland
- Paediatric and Reproductive Genetics UnitWomen's and Children's HospitalAdelaideSouth AustraliaAustralia
| | - Alicia B. Byrne
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
| | - Tristan S.E. Hardy
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- RepromedDulwichAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Milena Babic
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Jinghua Feng
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Thuong Ha
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Sarah L. King‐Smith
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
| | - Andreas W. Schreiber
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - April Crawford
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Nick Manton
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Lynette Moore
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Christopher P. Barnett
- Paediatric and Reproductive Genetics UnitWomen's and Children's HospitalAdelaideSouth AustraliaAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Hamish S. Scott
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
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