Title: Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Journal Article · · Journal of Medical Genetics

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Sponsoring Organization:
USDOE Office of Electricity (OE), Advanced Grid Research & Development. Power Systems Engineering Research
OSTI ID:
2336829
Journal Information:
Journal of Medical Genetics, Journal Name: Journal of Medical Genetics Journal Issue: 8 Vol. 61; ISSN 0022-2593
Publisher:
BMJCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (46)

Further delineation of Kabuki syndrome in 48 well‐defined new individuals journal December 2004
A de novo GJB2 (connexin 26) mutation, R75W, in a Chinese pedigree with hearing loss and palmoplantar keratoderma journal March 2009
Ocular albinism with infertility and late‐onset sensorineural hearing loss journal July 2018
Identification of novel MITF mutations in Chinese families with Waardenburg syndrome type II journal July 2021
Duchenne muscular dystrophy: Pathogenetic aspects and genetic prevention journal March 1984
DVPred: a disease-specific prediction tool for variant pathogenicity classification for hearing loss journal February 2022
Functional Mutation of SMAC/DIABLO, Encoding a Mitochondrial Proapoptotic Protein, Causes Human Progressive Hearing Loss DFNA64 journal July 2011
Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum journal June 2018
Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder journal April 2019
Genetics of cryptorchidism and testicular regression journal January 2022
Cryptorchidism concordance in monozygotic and dizygotic twin brothers, full brothers, and half-brothers journal January 2010
Identification of two novel missense WFS1 mutations, H696Y and R703H, in patients with non-syndromic low-frequency sensorineural hearing loss journal February 2011
Population-based investigation of familial undescended testis and its association with other urogenital anomalies journal December 2005
Acquired cryptorchidism: More harm than thought? journal August 2016
Urological Manifestations of Duchenne Muscular Dystrophy journal October 2013
Generation of Haploid Spermatids with Fertilization and Development Capacity from Human Spermatogonial Stem Cells of Cryptorchid Patients journal October 2014
Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus journal May 2022
The UK10K project identifies rare variants in health and disease journal September 2015
Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia journal April 2020
Duchenne muscular dystrophy journal February 2021
Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data journal February 2019
Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants journal March 2015
Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies journal April 2007
Familial Aggregation of Cryptorchidism--A Nationwide Cohort Study journal April 2008
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data: Table 1. journal February 2016
Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders journal June 2021
Pathway analysis supports association of nonsyndromic cryptorchidism with genetic loci linked to cytoskeleton-dependent functions journal July 2015
Duchenne Muscular Dystrophy journal March 2015
Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption journal September 2021
Isolation, Characterization, and Culture of Human Spermatogonia1 journal February 2010
The Epidemiology of Congenital Cryptorchidism, Testicular Ascent and Orchiopexy journal December 2003
Exome Sequencing Identifies a Novel Frameshift Mutation ofMYO6as the Cause of Autosomal Dominant Nonsyndromic Hearing Loss in a Chinese Family journal September 2014
Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome journal October 2022
Evolutionary evidence of the effect of rare variants on disease etiology journal September 2010
Familial bilateral cryptorchidism is caused by recessive variants in RXFP2 journal June 2019
Human X chromosome exome sequencing identifiesBCORL1as contributor to spermatogenesis journal May 2020
Population Genetics of Rare Variants and Complex Diseases journal January 2012
X-Linked Spinal Muscular Atrophy 2 due to a Synonymous Variant in the UBA1 Gene in a Family with Novel Findings from Turkey journal January 2022
Genes located in Y-chromosomal regions important for male fertility show altered transcript levels in cryptorchidism and respond to curative hormone treatment journal June 2019
Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders journal April 2021
The Ensembl Variant Effect Predictor journal June 2016
Anatomical and Functional Aspects of Testicular Descent and Cryptorchidism journal April 1997
Serum Androgen Bioactivity in Cryptorchid and Noncryptorchid Boys during the Postnatal Reproductive Hormone Surge journal June 2003
Rare variants regulate expression of nearby individual genes in multiple tissues journal June 2021
Testicular Cancer and Cryptorchidism journal January 2013
Rare variants contribute disproportionately to quantitative trait variation in yeast journal October 2019