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Zu B, Wang Z, Xu Y, You G, Fu Q. Nonframeshifting indel variations in polyalanine repeat of
HOXD13
gene underlies hereditary limb malformation for two Chinese families. Dev Dyn 2021; 250:1220-1228. [DOI: 10.1002/dvdy.310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bailing Zu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Zhigang Wang
- Department of Pediatric Orthopedic Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yunlan Xu
- Department of Pediatric Orthopedic Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Guoling You
- Department of Laboratory Medicine Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
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2
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A heterozygous duplication variant of the HOXD13 gene caused synpolydactyly type 1 with variable expressivity in a Chinese family. BMC MEDICAL GENETICS 2019; 20:203. [PMID: 31870337 PMCID: PMC6929446 DOI: 10.1186/s12881-019-0908-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/15/2019] [Indexed: 11/19/2022]
Abstract
Background Synpolydactyly type 1 (SPD1), also known as syndactyly type II, is an autosomal dominant limb deformity generally results in webbing of 3rd and 4th fingers, duplication of 4th or 5th toes. It is most commonly caused by mutation in HOXD13 gene. In this study, a five-generation Chinese family affected with SPD1 disease were collected. We tried to identify the pathogenic variations associated with SPD1 involved in the family. Methods We used the whole genome sequencing (WGS) to identify the pathogenic variant in this family which was later confirmed by PCR-Sanger sequencing. The genetic variation were evaluated with the frequencies in the 1000 Genome Project and Exome Aggregation Consortium (ExAC) dataset. The significance of variants were assessed using different mutation predictor softwares like Mutation Taster, PROVEAN and SIFT. The classification of variants was assessed according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed the mutation of 24-base pair duplication (c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC) in exon one of HOXD13 in heterozygous form which was predicted to result in eight extra alanine (A) residues in N-terminal domain of HOXD13 protein. The mutation was detected in all affected members of the family. Conclusion Based on our mutation analysis of variant c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC in HOXD13 and its cosegregation in all affected family members, we found this variant as likely pathogenic to this SPD1 family. Our study highlights variable expressivity of HOXD13 mutation. Our results also widen the spectrum of HOXD13 mutation responsible for SPD1.
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Guo X, Shi T, Lin M, Zhang Y. A Nonsense Mutation in HOXD13 Gene from A Chinese Family with Non-Syndromic Synpolydactyly. TOHOKU J EXP MED 2019; 249:93-100. [PMID: 31611522 DOI: 10.1620/tjem.249.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Synpolydactyly is a congenital limb malformation characterized by incomplete separation and duplication in fingers and/or toes, which is mainly caused by mutations in the homeobox D13 (HOXD13) gene. Here, a four-generation family with variant phenotypes of synpolydactyly was analyzed, in which the proband had bilateral preaxial synpolydactyly in toes with normal fingers, the father had clinodactyly in the fifth fingers, while the mother and grandma was normal. Trio whole-exome sequencing (trio-WES) is a high throughput sequencing targeting whole genome for detecting exonic variants from the proband and the parents in a family. Through trio-WES followed by Sanger sequencing and enzyme digestion, a heterozygous nonsense mutation (c.859 C>T/p.Gln287Ter) was newly identified in the homeodomain of the HOXD13 gene from the proband and the affected father, but not from the unaffected mother, the unaffected grandma, or the normal control. Mutation Taster, Human Splicing Finder and EX-SKIP predicted that the heterozygous mutation (c.859 C>T) would result in haploinsufficiency of HOXD13 protein through nonsense-mediated mRNA decay (NMD) and splicing abnormality, which might disrupt the integrity and reduce the expression level of the HOXD13 protein (loss-of-function). In short, a heterozygous nonsense mutation in the HOXD13 gene was newly identified in two patients with mild phenotypes of synpolydactyly, which extends the mutation spectrum in HOXD13 gene. Moreover, the findings we presented here deepen our understanding of the clinical consequences of non-syndromic synpolydactyly and may provide a new clue for further studies of the pathogenic mechanism of the mutation that causes aberrant splicing of HOXD13 gene.
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Affiliation(s)
- Xiaoyan Guo
- Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University
| | - Tengfei Shi
- Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University
| | - Mingrui Lin
- Intensive Care Unit, The Affiliated People's Hospital of Fujian Traditional Medical University
| | - Yiyuan Zhang
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University
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WITHDRAWN: A 24-base pair duplication in exon one of HOXD13 gene linked to synpolydactyly type 1 in a Chinese family. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions. Molecules 2017; 22:molecules22122027. [PMID: 29186753 PMCID: PMC6149999 DOI: 10.3390/molecules22122027] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins and proteins with intrinsically disordered regions have been shown to be highly prevalent in disease. Furthermore, disease-causing expansions of the regions containing tandem amino acid repeats often push repetitive proteins towards formation of irreversible aggregates. In fact, in disease-relevant proteins, the increased repeat length often positively correlates with the increased aggregation efficiency and the increased disease severity and penetrance, being negatively correlated with the age of disease onset. The major categories of repeat extensions involved in disease include poly-glutamine and poly-alanine homorepeats, which are often times located in the intrinsically disordered regions, as well as repeats in non-coding regions of genes typically encoding proteins with ordered structures. Repeats in such non-coding regions of genes can be expressed at the mRNA level. Although they can affect the expression levels of encoded proteins, they are not translated as parts of an affected protein and have no effect on its structure. However, in some cases, the repetitive mRNAs can be translated in a non-canonical manner, generating highly repetitive peptides of different length and amino acid composition. The repeat extension-caused aggregation of a repetitive protein may represent a pivotal step for its transformation into a proteotoxic entity that can lead to pathology. The goals of this article are to systematically analyze molecular mechanisms of the proteinopathies caused by the poly-glutamine and poly-alanine homorepeat expansion, as well as by the polypeptides generated as a result of the microsatellite expansions in non-coding gene regions and to examine the related proteins. We also present results of the analysis of the prevalence and functional roles of intrinsic disorder in proteins associated with pathological repeat expansions.
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Wang B, Li N, Geng J, Wang Z, Fu Q, Wang J, Xu Y. Exome sequencing identifies a novel nonsense mutation of HOXD13 in a Chinese family with synpolydactyly. Congenit Anom (Kyoto) 2017; 57:4-7. [PMID: 27254532 DOI: 10.1111/cga.12173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/30/2022]
Abstract
Synpolydactyly (SPD) is an autosomal dominant limb malformation with a distinctive combination of syndactyly and polydactyly. SPD is clinically heterogeneous and could be genetically classified into three types. The clinical phenotype of SPD is complicated by its variable expressivity. In the present study, whole exome sequencing (WES) was used to identify the affected gene(s) in a Chinese family with atypical SPD phenotype. Our results showed that a novel heterogenous nonsense mutation (c.556C > T, p.R186X) in HOXD13 was associated with this SPD case. Due to variable expressivity, the diagnosis of a clinical heterogenous disease such as SPD is usually difficult. Our results also suggested that WES is an efficient tool to assist with these diagnoses.
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Affiliation(s)
- Bo Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Geng
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhigang Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yunlan Xu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Zhou J, Chen Y, Cao K, Zou Y, Zhou H, Hu F, Ni B, Chen Y. Functional classification and mutation analysis of a synpolydactyly kindred. Exp Ther Med 2014; 8:1569-1574. [PMID: 25289061 PMCID: PMC4186389 DOI: 10.3892/etm.2014.1957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/07/2014] [Indexed: 01/30/2023] Open
Abstract
The aim of the present study was to analyze a congenital syndactyly/polydactyly kindred and propose a new functional classification method of clinical significance. The modes of inheritance and mutational mechanisms were also determined using genetic analyses. Hand and foot anatomy and functions were measured using photographic images, X-ray imaging and grip ability tests. Genetic analysis comprised the genotyping of polymorphic microsatellite markers at known polydactyly-associated loci and the sequencing of the candidate gene. A functional classification system was devised to divide the clinical features into three types, which included mild, moderate or severe deformity. The family was concluded to have syndactyly type II with autosomal dominant inheritance. The microsatellites, D2S2310 and D2S2314, at the 2q31–32 chromosome, which have previously been associated with synpolydactyly type I, were found to be associated with the disorder in the current family. A 27-bp insertion mutation was identified in the affected individuals in the HOXD13 gene at this locus. The insertion added a further nine alanine residues to the polyalanine stretch within the encoded protein. In conclusion, the functional classification method described in the present study may be used to guide surgical approaches to treatment. A family was identified in whom expansion of the polyalanine tract in the HOXD13 gene causes autosomal dominant hereditary synpolydactyly.
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Affiliation(s)
- Jianda Zhou
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yao Chen
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Ke Cao
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yonghua Zou
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Haiyan Zhou
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Feng Hu
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Bin Ni
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Yong Chen
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
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Dai L, Liu D, Song M, Xu X, Xiong G, Yang K, Zhang K, Meng H, Guo H, Bai Y. Mutations in the homeodomain of HOXD13 cause syndactyly type 1-c in two Chinese families. PLoS One 2014; 9:e96192. [PMID: 24789103 PMCID: PMC4006867 DOI: 10.1371/journal.pone.0096192] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Syndactyly type 1 (SD1) is an autosomal dominant limb malformation characterized in its classical form by complete or partial webbing between the third and fourth fingers and/or the second and third toes. Its four subtypes (a, b, c, and d) are defined based on variable phenotypes, but the responsible gene is yet to be identified. SD1-a has been mapped to chromosome 3p21.31 and SD1-b to 2q34–q36. SD1-c and SD1-d are very rare and, to our knowledge, no gene loci have been identified. Methods and Results In two Chinese families with SD1-c, linkage and haplotype analyses mapped the disease locus to 2q31-2q32. Copy number variation (CNV) analysis, using array-based comparative genomic hybridization (array CGH), excluded the possibility of microdeletion or microduplication. Sequence analyses of related syndactyly genes in this region identified c.917G>A (p.R306Q) in the homeodomain of HOXD13 in family A. Analysis on family B identified the mutation c.916C>G (p.R306G) and therefore confirmed the genetic homogeneity. Luciferase assays indicated that these two mutations affected the transcriptional activation ability of HOXD13. The spectrum of HOXD13 mutations suggested a close genotype-phenotype correlation between the different types of HOXD13-Syndactyly. Overlaps of the various phenotypes were found both among and within families carrying the HOXD13 mutation. Conclusions Mutations (p.R306Q and p.R306G) in the homeodomain of HOXD13 cause SD1-c. There are affinities between SD1-c and synpolydactyly. Different limb malformations due to distinct classes of HOXD13 mutations should be considered as a continuum of phenotypes and further classification of syndactyly should be done based on phenotype and genotype.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Dan Liu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Min Song
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Xueqing Xu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Gang Xiong
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kang Yang
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kun Zhang
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hui Meng
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
| | - Yun Bai
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
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Shi X, Ji C, Cao L, Wu Y, Shang Y, Wang W, Luo Y. A splice donor site mutation in HOXD13 underlies synpolydactyly with cortical bone thinning. Gene 2013; 532:297-301. [PMID: 24055421 DOI: 10.1016/j.gene.2013.09.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 08/08/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Synpolydactyly 1(SPD1) is a dominantly inherited distal limb anomaly that is characterized by incomplete digit separation and increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions and mutations in the homeodomain of the HOXD13. We report a splice donor site mutation in HOXD13 associated in most cases with cortical bone thinning. In vitro study of transcripts and truncated protein analysis indicated that c.781+1G>A mutation results in truncated HOXD13 protein p.G190fsX4. Luciferase assay indicated that the truncated HOXD13 protein failed to bind to DNA. The mechanism for this phenotype was truncated protein loss of function.
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Affiliation(s)
- Xiuyan Shi
- The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
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Brison N, Debeer P, Tylzanowski P. Joining the fingers: AHOXD13story. Dev Dyn 2013; 243:37-48. [DOI: 10.1002/dvdy.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nathalie Brison
- Center for Human Genetics; University Hospitals Leuven, University of Leuven; Belgium
| | - Philippe Debeer
- Department of Development and Regeneration; University of Leuven; Belgium
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