Regional missense constraint improves variant deleteriousness prediction

Cited by (354)

Items 201–300 of 354

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2. Evidence for the additivity of rare and common variant burden throughout the spectrum of intellectual disability
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3. Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance
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4. A deep learning model for prediction of autism status using whole-exome sequencing data
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5. One hundred thirty-four germ line PU.1 variants and the agammaglobulinemic patients carrying them
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6. Functionally constrained human proteins are less prone to mutational instability from single amino acid substitutions
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7. A probabilistic graphical model for estimating selection coefficients of nonsynonymous variants from human population sequence data
   Yige Zhao, Tian Lan, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy K. Chung, Yufeng Shen · 2025 · Nature Communications
8. De novo mutation hotspots in homologous protein domains identify function-altering mutations in neurodevelopmental disorders
   Laurens Wiel, Juliet E. Hampstead, Hanka Venselaar, Lisenka E.L.M. Vissers, Han G. Brunner, Rolph Pfundt, Gerrit Vriend, Joris A. Veltman, Christian Gilissen · 2022 · The American Journal of Human Genetics
9. Genetic intolerance analysis as a tool for protein science
   Geoffrey Li, Eliot T. C. Forster-Benson, Charles R. Sanders · 2019 · Biochimica et Biophysica Acta (BBA) - Biomembranes
10. A population-based approach for gene prioritization in understanding complex traits
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11. Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure: implications for variant effect prediction
    Lukas Gerasimavicius, Benjamin Livesey, Joseph A. Marsh · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
12. Meta-EA: a gene-specific combination of available computational tools for predicting missense variant effects
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13. Whole‐exome DNA sequencing in childhood anxiety disorders identifies rare de novo damaging coding variants
    Emily Olfson, Eli R. Lebowitz, Grace Hommel, Neha Dinesh Pashankar, Wendy K. Silverman, Thomas V. Fernandez · 2022 · Depression and Anxiety
14. Evidence of synergism among three genetic variants in a patient with LMNA-related lipodystrophy and amyotrophic lateral sclerosis leading to a remarkable nuclear phenotype
    Kathryn Volkening, Sali M.K. Farhan, Jessica Kao, Cheryl Leystra‐Lantz, Lee Cyn Ang, Adam D. McIntyre, Jian Wang, Robert Alexander Hegele, Michael Joseph Strong · 2021 · Molecular and Cellular Biochemistry
15. X-chromosome inactivation and PCDH19-associated epileptic encephalopathy: A novel PCDH19 variant in a Chinese family
    Ling-Yin Hung, Shreenidhi Ranganatha Subramaniam, Tsz‐Yan Tammy Tong, Wing-Ki Chan, Eric Kin‐Cheong Yau, Chor-Kwan Ching · 2021 · Clinica Chimica Acta
16. Ultrarare Missense Variants Implicated in Utah Pedigrees Multiply Affected With Schizophrenia
    Cathal Ormond, Niamh Ryan, Elizabeth A. Heron, Michael Gill, William Byerley, Aiden Peter Corvin · 2023 · Biological Psychiatry Global Open Science
17. Polygenic and developmental profiles of autism differ by age at diagnosis
    Xinhe Zhang, Jakob Grove, Yuanjun Gu, Cornelia K. Buus, Lea K. Nielsen, Sharon Neufeld, Mahmoud Koko, Daniel Shiloh Malawsky, Emma M. Wade, Ellen Verhoef et al. · 2024 · medRxiv
18. Expanding the utility of variant effect predictions with phenotype-specific models
    David F. Stein, Meltem Ece Kars, Baptiste Milisavljevic, Matthew E. Mort, Peter D. Stenson, Jean‐Laurent Casanova, D.N. Cooper, Bertrand Boisson, Peng Zhang, Avner Schlessinger et al. · 2025 · Nature Communications
19. Genomic and Developmental Models to Predict Cognitive and Adaptive Outcomes in Autistic Children
    Vincent-Raphaël Bourque, Zoe Schmilovich, Guillaume Huguet, Jade England, Adeniran Okewole, Cécile Poulain, Thomas Renne, Martineau Jean‐Louis, Zohra Saci, Xinhe Zhang et al. · 2025 · Archives of Pediatrics and Adolescent Medicine
20. Potential involvement of DSCAML1 mutations in neurodevelopmental disorders
    Shigehiro Ogata, Koichi Hashizume, Yoneko Hayase, Yukie Kanno, Kei Hori, Shabeesh Balan, Takeo Yoshikawa, Hidehiko Takahashi, Shinichiro Taya, Mikio Hoshino · 2021 · Genes to Cells
21. Disruption of RFX family transcription factors causes autism, attention deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior
    Holly K. Harris, Tojo Nakayama, Jenny F. Lai, Boxun Zhao, Nikoleta Argyrou, Cynthia Sophia Gubbels, Aubrie Soucy, Casie A. Genetti, Lance H. Rodan, George E. Tiller et al. · 2020 · medRxiv
22. Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery
    Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline Fiona Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware · 2022 · medRxiv
23. Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes
    Dilliott, Allison A, Kwon, Seulki, Rouleau, Guy A, Iqbal, Sumaiya, Farhan, Sali M K · 2023 · Brain
24. Structural plasticity of the coiled–coil interactions in human SFPQ
    Heidar J Koning, Jia Y. Lai, Andrew C. Marshall, Elke Ströher, Gavin Monahan, Anuradha Pullakhandam, Gavin J. Knott, Timothy M Ryan, Archa H. Fox, Andrew E. Whitten et al. · 2024 · Nucleic Acids Research
25. Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network
    Narumi Hatano, Mayumi Kamada, Ryosuke Kojima, Yasushi Okuno · 2023 · BMC Bioinformatics
26. Comparison of three bioinformatics tools in the detection of ASD candidate variants from whole exome sequencing data
    Apurba Shil, Liron Levin, Hava M. Golan, Gal Meiri, Analya Michaelovski, Yair Sadaka, Adi Avniel Aran, Ilan Dinstein, Idan Menashe · 2023 · Scientific Reports
27. In silico versus functional characterization of genetic variants: lessons from muscle channelopathies
    Vinojini Vivekanandam, Rebecca Ellmers, Dipa L. Jayaseelan, Henry Houlden, Roope Männikkö, Michael G. Hanna · 2022 · Brain
28. Evaluation of familial phenotype deviation to measure the impact of de novo mutations in autism
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29. Deleterious coding variation associated with autism is shared across ancestries
    Marina Natividad Avila, Seulgi Jung, F. Kyle Satterstrom, Jack M. Fu, Tess Levy, Laura Gail Sloofman, Lambertus Klei, Thariana Pichardo, Dalia Yesenia Palafox Márquez., Christine R. Stevens et al. · 2026 · Nature Medicine
30. Evaluating the use of paralogous protein domains to increase data availability for missense variant classification
    Adam C. Gunning, Caroline Fiona Wright · 2023 · Genome Medicine
31. Identifying somatic driver mutations in cancer with a language model of the human genome
    Guangjian Zeng, Chengzhi Zhao, Guanpeng Li, Zhengyang Huang, Jinhu Zhuang, Xiaohua Liang, Xiaxia Yu, Shenying Fang · 2025 · Computational and Structural Biotechnology Journal
32. Oxytocin Exposure in Labor and its Relationship with Cognitive Impairment and the Genetic Architecture of Autism
    Alicia García-Alcón, Javier González‐Peñas, Elisa Weckx, María José Penzol, Xaquín Gurriarán, Javier Costas, Covadonga M. Díaz‐Caneja, Carmen Moreno, Patricia Andrea Hernandez, Celso Arango et al. · 2022 · Journal of Autism and Developmental Disorders
33. Cochlear nerve deficiency in SOX11 ‐related Coffin‐Siris syndrome
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34. Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders
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35. m 6 A ‐ mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly
    Sierra S. Nishizaki, Nicholas K. Haghani, Gabriana N. La, Natasha Ann F. Mariano, José M. Uribe‐Salazar, Gulhan Kaya, Melissa Regester, Derek Sayre Andrews, Christine Wu Nordahl, David G. Amaral et al. · 2025 · Autism Research
36. Identification of pathogenic variant enriched regions across genes and gene families
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37. Single cell sequencing as a general variant interpretation assay
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38. Autism mutations rewire protein interaction networks to drive neurodevelopmental pathology
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39. Polygenic scores stratify neurodevelopmental copy number variant carrier cognitive outcomes in the UK Biobank
    Thomas J. Dinneen, Fiana Ní Ghrálaigh, Cathal Ormond, Elizabeth A. Heron, George Kirov, Lorna M. Lopez, Louise Gallagher · 2024 · npj Genomic Medicine
40. MIRAGE: A Bayesian statistical method for gene-level rare-variant analysis incorporating functional annotations
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41. Genetic signature detected in T cell receptors from patients with severe COVID-19
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42. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
    Enrique Audain, Anna Wilsdon, Gregor Dombrowsky, Alejandro Sifrim, Jeroen Breckpot, Yasset Pérez‐Riverol, Siobhan Loughna, Allan Daly, Pavlos Antoniou, P. Hofmann et al. · 2026 · npj Genomic Medicine
43. Integrating rare variant genetics and brain transcriptome data implicates novel schizophrenia putative risk genes
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44. From prioritisation to understanding: mechanistic predictions of variant effects
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45. Age dependent association of inbreeding with risk for schizophrenia in Egypt
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46. Identification of moderate effect size genes in autism spectrum disorder through a novel gene pairing approach
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47. Contribution of rare and common variants to intellectual disability in a high-risk population sub-isolate of Northern Finland
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48. A framework for integrated clinical risk assessment using population sequencing data
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49. Rare schizophrenia risk variant burden is conserved in diverse human populations
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50. Dissecting the contribution of common variants to risk of rare neurodevelopmental conditions
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51. Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis
    Ryo Morikawa, Yuichiro Watanabe, Hirofumi Igeta, Reza K. Arta, Masashi Ikeda, Satoshi Okazaki, Satoshi Hoya, Takeo Saito, Ikuo Otsuka, Jun Egawa et al. · 2022 · Psychiatry Research
52. Brief Report: Risk Variants Could Inform Early Neurodevelopmental Outcome in Children with Developmental Disabilities
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53. Estimating clinical risk in gene regions from population sequencing cohort data
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54. Whole-exome sequencing reveals an association of rs112065068 in TGOLN2 gene with distant metastasis of non-small cell lung cancer
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55. A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
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57. CR1 variants contribute to FSGS susceptibility across multiple populations
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58. Evaluating variant pathogenicity prediction tools to establish African inclusive guidelines for germline genetic testing
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59. Inherited bone marrow failure with macrothrombocytopenia due to germline tubulin beta class I (TUBB) variant
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60. Burden re-analysis of neurodevelopmental disorder cohorts for prioritization of candidate genes
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61. M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits
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62. Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
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63. Substantial role of rare inherited variation in individuals with developmental disorders
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64. Investigating the Interplay Between Prematurity and Genetic Variation in the Context of Rare Developmental Disorders
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65. Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders
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66. Common and Rare Variant Genetic Contributions in African Americans With Autism
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68. QAFI: a novel method for quantitative estimation of missense variant impact using protein-specific predictors and ensemble learning
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69. Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing
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70. An ensemble machine learning-based performance evaluation identifies top In-Silico pathogenicity prediction methods that best classify driver mutations in cancer
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71. Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant-effect predictors
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72. Systematic Assessment of Protein C-Termini Mutated in Human Disorders
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73. How human genetic context can inform pathogenicity classification: FGFR1 variation in idiopathic hypogonadotropic hypogonadism
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74. Genetic architecture of postpartum psychosis: from common to rare genetic variation
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75. Analyses of rare and common alleles in parent-proband trios implicate rare missense variants in SLC6A1 in schizophrenia and confirm the involvement of loss of function intolerant and neurodevelopmental disorder genes
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76. The 3D spatial constraint on 6.1 million amino acid sites in the human proteome
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77. Haploinsufficiency underlies the neurodevelopmental consequences of SLC6A1 /GAT-1 variants
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80. Investigating the role of common cis -regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders
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84. BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees
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85. An integrative scoring approach for prioritization of rare autism spectrum disorder candidate variants from whole exome sequencing data
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86. Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders
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88. Common and rare genetic variant associations with cognitive performance across development in British birth cohorts
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89. A domain damage index to prioritizing the pathogenicity of missense variants
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90. Case report: Somatic mutations in microtubule dynamics-associated genes in patients with WNT-medulloblastoma tumors
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91. Exploring somatic mutations in BRAF, KRAS, and NRAS as therapeutic targets in Saudi colorectal cancer patients through massive parallel sequencing and variant classification
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92. Association of IgG4-related disease with human inborn errors of immunity
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93. Functional consequences of calmodulin variants identified among schizophrenia patients and controls
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94. Assessing predictions on fitness effects of missense variants in HMBS in CAGI6
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95. The Genetic Landscape of Diamond-Blackfan Anemia
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96. Sarm1 Haploinsufficiency and Low Expression Levels after Antisense Oligonucleotides Delays Programmed Axon Degeneration
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97. Faculty Opinions recommendation of Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.
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98. Ultra-rare de novo damaging coding variants are enriched in attention-deficit/hyperactivity disorder and identify risk genes
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99. Federated analysis of the contribution of recessive coding variants to 29,745 developmental disorder patients from diverse populations
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