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JOURNAL ARTICLE
Yuqi Shao, Saisai Yang, Jiafu Li, Lin Cheng, Jiawei Kang, Juan Liu, Jianhong Ma, Jie Duan, Yuanzhen Zhang
Objective: The article aims to provide genetic counseling to a family with two children who were experiencing growth and developmental delays. Methods: Clinical information of the proband was collected. Peripheral blood was collected from core family members to identify the initial reason for growth and developmental delays by whole exome sequencing (WES) and Sanger sequencing. To ascertain the consequences of the newly discovered variants, details of the variants detected were analyzed by bioinformatic tools...
2024: Frontiers in Genetics
#2
JOURNAL ARTICLE
Xuanjin Du, Chunyan Wang, Jialu Liu, Minghui Yu, Haixin Ju, Shanshan Xue, Yaxin Li, Jiaojiao Liu, Rufeng Dai, Jing Chen, Yihui Zhai, Jia Rao, Xiang Wang, Yubo Sun, Lei Sun, Xiaohui Wu, Hong Xu, Qian Shen
BACKGROUND: Congenital anomalies of the kidney and urinary tract (CAKUT) are prevalent birth defects. Although pathogenic CAKUT genes are known, they are insufficient to reveal the causes for all patients. Our previous studies indicated GEN1 as a pathogenic gene of CAKUT in mice, and this study further investigated the correlation between GEN1 and human CAKUT. METHODS: In this study, DNA from 910 individuals with CAKUT was collected; 26 GEN1 rare variants were identified, and two GEN1 (missense) variants in a non-CAKUT group were found...
April 24, 2024: Human Genomics
#3
JOURNAL ARTICLE
Rawda Naamneh Elzenaty, Idoia Martinez de Lapiscina, Chrysanthi Kouri, Kay-Sara Sauter, Grit Sommer, Luis Castaño, Christa E Flück
CONTEXT: Steroidogenic factor 1 (NR5A1/SF-1) is a nuclear receptor that regulates sex development, steroidogenesis and reproduction. Genetic variants in NR5A1/SF-1 are common among differences of sex development (DSD) and associate with a wide range of phenotypes, but their pathogenic mechanisms remain unclear. OBJECTIVE: Novel, likely disease-causing NR5A1/SF-1 variants from the SF1next cohort of individuals with DSD were characterized to elucidate their pathogenic effect...
April 16, 2024: Journal of Clinical Endocrinology and Metabolism
#4
REVIEW
Miguel Correa Marrero, Jürgen Jänes, Delora Baptista, Pedro Beltrao
The last five years have seen impressive progress in deep learning models applied to protein research. Most notably, sequence-based structure predictions have seen transformative gains in the form of AlphaFold2 and related approaches. Millions of missense protein variants in the human population lack annotations, and these computational methods are a valuable means to prioritize variants for further analysis. Here, we review the recent progress in deep learning models applied to the prediction of protein structure and protein variants, with particular emphasis on their implications for human genetics and health...
April 15, 2024: Annual Review of Genomics and Human Genetics
#5
JOURNAL ARTICLE
Yongli Zhang, Yuwei Zhao, Liying Dai, Yu Liu, Zifeng Shi
BACKGROUND: Auriculocondylar syndrome (ARCND) is a rare congenital craniofacial developmental malformation syndrome of the first and second pharyngeal arches with external ear malformation at the junction between the lobe and helix, micromaxillary malformation, and mandibular condylar hypoplasia. Four subtypes of ARCND have been described so far, that is, ARCND1 (OMIM # 602483), ARCND2 (ARCND2A, OMIM # 614669; ARCND2B, OMIM # 620458), ARCND3 (OMIM # 615706), and ARCND4 (OMIM # 620457)...
April 2024: Molecular Genetics & Genomic Medicine
#6
JOURNAL ARTICLE
Stuart A MacGowan, Fábio Madeira, Thiago Britto-Borges, Geoffrey J Barton
Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES)...
April 11, 2024: Communications Biology
#7
JOURNAL ARTICLE
Junwen Wang, Yingwei Wang, Yi Jiang, Shiqiang Li, Xiaoyun Jia, Xueshan Xiao, Wenmin Sun, Panfeng Wang, Qingjiong Zhang
PURPOSE: Heterozygous variants of IMPDH1 are associated with autosomal dominant retinitis pigmentosa (adRP). The current study aims to investigate the characteristics of the adRP-associated variants. METHODS: IMPDH1 variants from our exome sequencing dataset were retrieved and systemically evaluated through multiple online prediction tools, comparative genomics (in-house dataset, HGMD, and gnomAD), and phenotypic association. Potential pathogenic variants (PPVs) were further confirmed by Sanger sequencing and segregation analysis...
April 11, 2024: Current Eye Research
#8
JOURNAL ARTICLE
Kian Hong Kock, Patrick K Kimes, Stephen S Gisselbrecht, Sachi Inukai, Sabrina K Phanor, James T Anderson, Gayatri Ramakrishnan, Colin H Lipper, Dongyuan Song, Jesse V Kurland, Julia M Rogers, Raehoon Jeong, Stephen C Blacklow, Rafael A Irizarry, Martha L Bulyk
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity...
April 10, 2024: Nature Communications
#9
JOURNAL ARTICLE
Soumia Brakta, Quansheng Du, Lynn P Chorich, Zoe A Hawkins, Megan E Sullivan, Eun Kyung Ko, Hyung-Goo Kim, James Knight, Hugh S Taylor, Michael Friez, John A Phillips, Lawrence C Layman
The molecular basis of mullerian aplasia, also known as Mayer-Rokitansky-Kuster Hauser (MRKH) or congenital absence of the uterus and vagina, is largely unknown. We applied a multifaceted genetic approach to studying the pathogenesis of MRKH including exome sequencing of trios and duos, genome sequencing of families, qPCR, RT-PCR, and Sanger sequencing to detect intragenic deletions, insertions, splice variants, single nucleotide variants, and rearrangements in 132 persons with MRKH. We identified two heterozygous variants in ZNHIT3 localized to a commonly involved CNV region at chromosome 17q12 in two different families with MRKH...
April 8, 2024: Molecular and Cellular Endocrinology
#10
James L Shepherdson, David M Granas, Jie Li, Zara Shariff, Stephen P Plassmeyer, Alex S Holehouse, Michael A White, Barak A Cohen
Cone-Rod Homeobox, encoded by CRX , is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS)...
March 27, 2024: bioRxiv
#11
JOURNAL ARTICLE
Weining Lin, Jude Wells, Zeyuan Wang, Christine Orengo, Andrew C R Martin
Computational approaches for predicting the pathogenicity of genetic variants have advanced in recent years. These methods enable researchers to determine the possible clinical impact of rare and novel variants. Historically these prediction methods used hand-crafted features based on structural, evolutionary, or physiochemical properties of the variant. In this study we propose a novel framework that leverages the power of pre-trained protein language models to predict variant pathogenicity. We show that our approach VariPred (Variant impact Predictor) outperforms current state-of-the-art methods by using an end-to-end model that only requires the protein sequence as input...
April 7, 2024: Scientific Reports
#12
JOURNAL ARTICLE
Maolin Ding, Ken Chen, Yuedong Yang, Huiying Zhao
Genetic diseases are mostly implicated with genetic variants, including missense, synonymous, non-sense, and copy number variants. These different kinds of variants are indicated to affect phenotypes in various ways from previous studies. It remains essential but challenging to understand the functional consequences of these genetic variants, especially the noncoding ones, due to the lack of corresponding annotations. While many computational methods have been proposed to identify the risk variants. Most of them have only curated DNA-level and protein-level annotations to predict the pathogenicity of the variants, and others have been restricted to missense variants exclusively...
April 4, 2024: Human Genetics
#13
JOURNAL ARTICLE
Zain Dardas, Jawid M Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M Grochowski, Edward G Jones, Shalini N Jhangiani, Xander H T Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E Posey, Donna M Muzny, Richard A Gibbs, James R Lupski, Zeynep Coban-Akdemir, Shaine A Morris
BACKGROUND: NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects. METHODS: We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses...
April 3, 2024: Genome Medicine
#14
JOURNAL ARTICLE
Wenqing Lu, Yong Li, Lanlan Meng, Chen Tan, Hongchuan Nie, Qianjun Zhang, Yuying Song, Huan Zhang, Yue-Qiu Tan, Chaofeng Tu, Haichun Guo, Longxiang Wu, Juan Du
PURPOSE: This study aimed to identify the genetic causes of male infertility and primary ciliary dyskinesia (PCD)/PCD-like phenotypes in three unrelated Han Chinese families. METHODS: We conducted whole-exome sequencing of three patients with male infertility and PCD/PCD-like phenotypes from three unrelated Chinese families. Ultrastructural and immunostaining analyses of patient spermatozoa and respiratory cilia and in vitro analyses were performed to analyze the effects of SPEF2 variants...
April 3, 2024: Journal of Assisted Reproduction and Genetics
#15
JOURNAL ARTICLE
Sadhna Rao, Anastasiia Sadybekov, David C DeWitt, Joanna Lipka, Vsevolod Katritch, Bruce E Herring
BACKGROUND: Glutamatergic synapse dysfunction is believed to underlie the development of Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) in many individuals. However, identification of genetic markers that contribute to synaptic dysfunction in these individuals is notoriously difficult. Based on genomic analysis, structural modeling, and functional data, we recently established the involvement of the TRIO-RAC1 pathway in ASD and ID. Furthermore, we identified a pathological de novo missense mutation hotspot in TRIO's GEF1 domain...
April 3, 2024: Molecular Autism
#16
JOURNAL ARTICLE
Sukanya Banerjee, Bishan Dass Radotra, Manni Luthra-Guptasarma, Manoj K Goyal
BACKGROUND: Limb Girdle Muscular Dystrophy R1 (LGMDR1) is an autosomal recessive neuromuscular disease caused by mutations in the calpain-3 (CAPN3) gene. As clinical and pathological features may overlap with other types of LGMD, therefore definite molecular diagnosis is required to understand the progression of this debilitating disease. This study aims to identify novel variants of CAPN3 gene in LGMDR1 patients. RESULTS: Thirty-four patients with clinical and histopathological features suggestive of LGMD were studied...
April 1, 2024: Orphanet Journal of Rare Diseases
#17
JOURNAL ARTICLE
Xuechen Tang, Nadine J Ortner, Yuliia V Nikonishyna, Monica L Fernández-Quintero, Janik Kokot, Jörg Striessnig, Klaus R Liedl
Voltage-gated L-type Cav1.3 Ca2+ channels support numerous physiological functions including neuronal excitability, sinoatrial node pacemaking, hearing, and hormone secretion. De novo missense mutations in the gene of their pore-forming α1-subunit (CACNA1D) induce severe gating defects which lead to autism spectrum disorder and a more severe neurological disorder with and without endocrine symptoms. The number of CACNA1D variants reported is constantly rising, but their pathogenic potential often remains unclear, which complicates clinical decision-making...
March 29, 2024: European Journal of Human Genetics: EJHG
#18
JOURNAL ARTICLE
Josephina A N Meester, Anne Hebert, Maaike Bastiaansen, Laura Rabaut, Jarl Bastianen, Nele Boeckx, Kathryn Ashcroft, Paldeep S Atwal, Antoine Benichou, Clarisse Billon, Jan D Blankensteijn, Paul Brennan, Stephanie A Bucks, Ian M Campbell, Solène Conrad, Stephanie L Curtis, Majed Dasouki, Carolyn L Dent, James Eden, Himanshu Goel, Verity Hartill, Arjan C Houweling, Bertrand Isidor, Nicola Jackson, Pieter Koopman, Anita Korpioja, Minna Kraatari-Tiri, Liina Kuulavainen, Kelvin Lee, Karen J Low, Alan C Lu, Morgan L McManus, Stephen P Oakley, James Oliver, Nicole M Organ, Eline Overwater, Nicole Revencu, Alison H Trainer, Bhavya Trivedi, Claire L S Turner, Rebecca Whittington, Andreas Zankl, Dominica Zentner, Lut Van Laer, Aline Verstraeten, Bart L Loeys
Pathogenic loss-of-function variants in BGN, an X-linked gene encoding biglycan, are associated with Meester-Loeys syndrome (MRLS), a thoracic aortic aneurysm/dissection syndrome. Since the initial publication of five probands in 2017, we have considerably expanded our MRLS cohort to a total of 18 probands (16 males and 2 females). Segregation analyses identified 36 additional BGN variant-harboring family members (9 males and 27 females). The identified BGN variants were shown to lead to loss-of-function by cDNA and Western Blot analyses of skin fibroblasts or were strongly predicted to lead to loss-of-function based on the nature of the variant...
March 26, 2024: NPJ Genomic Medicine
#19
JOURNAL ARTICLE
Qinghong Lin, Xuejun Wang, Xin Zhan, Xiaoliao Peng, Yan Wang, Xingtao Zhou
Here, we have reported the genetic and clinical characteristics of four generations of a family patient from China with congenital fibrosis of extraocular muscles 1 (CFEOM1) and keratoconus (KC). The history of diseases, clinical observations, and blood samples of all family members were collected. A total of 100 healthy participants were recruited as normal controls. The whole exome sequencing of the genomic DNA and polymerase chain reaction were performed on samples obtained from the controls and their family members to verify the gene variants...
March 30, 2024: Heliyon
#20
JOURNAL ARTICLE
Nan-Xiang Shen, Xiao-Chong Qu, Jing Yu, Cui-Xia Fan, Fu-Li Min, Ling-Ying Li, Ming-Rui Zhang, Bing-Mei Li, Jie Wang, Na He, Wei-Ping Liao, Yi-Wu Shi, Wen-Bin Li
NUS1 encodes the Nogo-B receptor, a critical regulator for unfolded protein reaction (UPR) signaling. Although several loss-of-function variants of NUS1 have been identified in patients with developmental and epileptic encephalopathy (DEE), the role of the NUS1 variant in Lennox-Gastaut syndrome (LGS), a severe child-onset DEE, remains unknown. In this study, we identified two de novo variants of NUS1, a missense variant (c.868 C > T/p.R290C) and a splice site variant (c.792-2 A > G), in two unrelated LGS patients using trio-based whole-exome sequencing performed in a cohort of 165 LGS patients...
March 23, 2024: Molecular Neurobiology
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