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Gene family information facilitates variant interpretation and identification of disease-associated genes

https://doi.org/10.1101/159780
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Current Protocols in Human Genetics
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Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
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The Human Intermediate Filament Database: comprehensive information on a gene family involved in many human diseases
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Paralogous annotation of disease-causing variants in long QT syndrome genes
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dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs
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Evolutionary constraints on structural similarity in orthologs and paralogs
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De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies
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Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication
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Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study
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De novo mutations in epileptic encephalopathies
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De novo mutations in schizophrenia implicate synaptic networks
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Synaptic, transcriptional and chromatin genes disrupted in autism
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The contribution of de novo coding mutations to autism spectrum disorder
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Large-scale discovery of novel genetic causes of developmental disorders
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A global reference for human genetic variation
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Analysis of protein-coding genetic variation in 60,706 humans
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Prevalence and architecture of de novo mutations in developmental disorders
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Exposing the fitness contribution of duplicated genes
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The Genotype-Tissue Expression (GTEx) project
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A general framework for estimating the relative pathogenicity of human genetic variants
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A framework for the interpretation of de novo mutation in human disease
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Prospective functional classification of all possible missense variants in PPARG
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Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples
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A method and server for predicting damaging missense mutations
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Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability
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Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
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Kinase mutations in human disease: interpreting genotype–phenotype relationships
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New genes as drivers of phenotypic evolution
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CHD5, a new member of the chromodomain gene family, is preferentially expressed in the nervous system
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Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability
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Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
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Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
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Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btv112openalex-snapshot
Unified representation of genetic variants
inferredcites →https://doi.org/10.1093/database/bar030openalex-snapshot
Ensembl BioMarts: a hub for data retrieval across taxonomic space
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On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkp829openalex-snapshot
Sequence-non-specific effects of RNA interference triggers and microRNA regulators
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Current status and new features of the Consensus Coding Sequence database
inferredcites →https://doi.org/10.1093/nar/gkv1222openalex-snapshot
ClinVar: public archive of interpretations of clinically relevant variants
inferredcites →https://doi.org/10.1101/gr.073585.107openalex-snapshot
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
inferredcites →https://doi.org/10.1101/gr.102210.109openalex-snapshot
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
inferredcites →https://doi.org/10.1126/science.aac9396openalex-snapshot
De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies
inferredcites →https://doi.org/10.1136/jmedgenet-2013-101917openalex-snapshot
Paralogue annotation identifies novel pathogenic variants in patients with Brugada syndrome and catecholaminergic polymorphic ventricular tachycardia
inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114725openalex-snapshot
Orthologs, Paralogs, and Evolutionary Genomics
inferredcites →https://doi.org/10.1186/s13059-016-0912-5openalex-snapshot
Spatiotemporal variation of mammalian protein complex stoichiometries
inferredcites →https://doi.org/10.1371/journal.pcbi.1004559openalex-snapshot
Gene Expression Switching of Receptor Subunits in Human Brain Development
inferredcites →https://doi.org/10.2307/2412448openalex-snapshot
Distinguishing Homologous from Analogous Proteins

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/humu.23798openalex-snapshot
MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains
inferred← citeshttps://doi.org/10.1002/mgg3.1309openalex-snapshot
The role of sodium channels in sudden unexpected death in pediatrics
inferred← citeshttps://doi.org/10.1016/j.biopsych.2018.08.022openalex-snapshot
Targeted Sequencing of 10,198 Samples Confirms Abnormalities in Neuronal Activity and Implicates Voltage-Gated Sodium Channels in Schizophrenia Pathogenesis
inferred← citeshttps://doi.org/10.1016/j.ejpn.2019.12.001openalex-snapshot
Time to move beyond genetics towards biomedical data-driven translational genomic research in severe paediatric epilepsies
inferred← citeshttps://doi.org/10.1101/2023.08.07.552236openalex-snapshot
Variant annotation across homologous proteins (“Paralogue Annotation”) identifies disease-causing missense variants with high precision, and is widely applicable across protein families
inferred← citeshttps://doi.org/10.1101/246850openalex-snapshot
Association between schizophrenia and both loss of function and missense mutations in paralog conserved sites of voltage-gated sodium channels
inferred← citeshttps://doi.org/10.1101/641043openalex-snapshot
Identification of pathogenic variant enriched regions across genes and gene families
inferred← citeshttps://doi.org/10.1101/671453openalex-snapshot
Predicting Functional Effects of Missense Variants in Voltage-Gated Sodium and Calcium Channels
inferred← citeshttps://doi.org/10.1101/gr.252601.119openalex-snapshot
Identification of pathogenic variant enriched regions across genes and gene families
inferred← citeshttps://doi.org/10.1111/dmcn.14519openalex-snapshot
Sodium channel epilepsies and neurodevelopmental disorders: from disease mechanisms to clinical application
inferred← citeshttps://doi.org/10.1111/epi.14705openalex-snapshot
The spectrum of intermediate SCN 8A‐related epilepsy
inferred← citeshttps://doi.org/10.1111/epi.14731openalex-snapshot
SCN 2A channelopathies: Mechanisms and models
inferred← citeshttps://doi.org/10.1111/epi.16438openalex-snapshot
Biological concepts in human sodium channel epilepsies and their relevance in clinical practice
inferred← citeshttps://doi.org/10.1126/scitranslmed.aay6848openalex-snapshot
Predicting functional effects of missense variants in voltage-gated sodium and calcium channels
inferred← citeshttps://doi.org/10.1186/s13073-019-0700-4openalex-snapshot
Keeping up with the genomes: scaling genomic variant interpretation
inferred← citeshttps://doi.org/10.1186/s13073-020-00725-6openalex-snapshot
Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders
inferred← citeshttps://doi.org/10.1212/wnl.0000000000007089openalex-snapshot
Clinical spectrum of STX1B -related epileptic disorders
inferred← citeshttps://doi.org/10.3410/f.735057908.793581708openalex-snapshot
Faculty Opinions recommendation of Clinical spectrum of STX1B-related epileptic disorders.
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