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Characterizing and comparing missense variants in monogenic disease and in cancer

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What this work says

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

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Human Gene Mutation Database (HGMD®): 2003 update

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SNPs, protein structure, and disease

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dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

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Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST‐Indel)

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Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N‐acetyl‐glucosaminidase) and UBE2I (Human SUMO‐ligase) challenges

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Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency

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The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies

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Protein stability and in vivo concentration of missense mutations in phenylalanine hydroxylase

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Conservation and prediction of solvent accessibility in protein families

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Knowledge‐based protein secondary structure assignment

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An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families

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The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

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Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

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Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

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Protein Thermostability Calculations Using Alchemical Free Energy Simulations

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In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

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Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

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Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

inferredcites →https://doi.org/10.1016/j.jmb.2005.08.020openalex-snapshot

Loss of Protein Structure Stability as a Major Causative Factor in Monogenic Disease

inferredcites →https://doi.org/10.1016/j.jmb.2005.12.025openalex-snapshot

Identification and Analysis of Deleterious Human SNPs

inferredcites →https://doi.org/10.1016/j.jmb.2011.06.046openalex-snapshot

Structural and Functional Impact of Cancer-Related Missense Somatic Mutations

inferredcites →https://doi.org/10.1021/ct400486popenalex-snapshot

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

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Molecular portraits of human breast tumours

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Oncogenic kinase signalling

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The Age Distribution of Cancer and a Multi-stage Theory of Carcinogenesis

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Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

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Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

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Comprehensive genomic characterization defines human glioblastoma genes and core pathways

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Comprehensive molecular characterization of human colon and rectal cancer

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Comprehensive genomic characterization of squamous cell lung cancers

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Comprehensive molecular portraits of human breast tumours

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Integrated genomic characterization of endometrial carcinoma

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Signatures of mutational processes in human cancer

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Discovery and saturation analysis of cancer genes across 21 tumour types

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Emerging landscape of oncogenic signatures across human cancers

inferredcites →https://doi.org/10.1038/ng.2892openalex-snapshot

A general framework for estimating the relative pathogenicity of human genetic variants

inferredcites →https://doi.org/10.1038/ng.3168openalex-snapshot

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

inferredcites →https://doi.org/10.1038/nmeth0410-248openalex-snapshot

A method and server for predicting damaging missense mutations

inferredcites →https://doi.org/10.1038/nrc1299openalex-snapshot

A census of human cancer genes

inferredcites →https://doi.org/10.1038/nrg3046openalex-snapshot

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

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The age distribution of cancer and a multi-stage theory of carcinogenesis

inferredcites →https://doi.org/10.1038/srep02650openalex-snapshot

Comprehensive identification of mutational cancer driver genes across 12 tumor types

inferredcites →https://doi.org/10.1039/c1mb05246bopenalex-snapshot

Is there a biological cost of protein disorder? Analysis of cancer-associated mutations

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Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

inferredcites →https://doi.org/10.1073/pnas.0701361104openalex-snapshot

The human disease network

inferredcites →https://doi.org/10.1073/pnas.0907710106openalex-snapshot

Toward a quantitative theory of intrinsically disordered proteins and their function

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Impact of deleterious passenger mutations on cancer progression

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Evaluating the evaluation of cancer driver genes

inferredcites →https://doi.org/10.1073/pnas.232565499openalex-snapshot

Dobzhansky–Muller incompatibilities in protein evolution

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Are Rare Variants Responsible for Susceptibility to Complex Diseases?

inferredcites →https://doi.org/10.1093/bioinformatics/btl390openalex-snapshot

Global topological features of cancer proteins in the human interactome

inferredcites →https://doi.org/10.1093/bioinformatics/btr357openalex-snapshot

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

inferredcites →https://doi.org/10.1093/bioinformatics/btt182openalex-snapshot

Predicting the functional consequences of cancer-associated amino acid substitutions

inferredcites →https://doi.org/10.1093/bioinformatics/btt395openalex-snapshot

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

inferredcites →https://doi.org/10.1093/bioinformatics/btu744openalex-snapshot

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

inferredcites →https://doi.org/10.1093/bioinformatics/btv430openalex-snapshot

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data

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Reduced collagen VI causes Bethlem myopathy: a heterozygous COL6A1 nonsense mutation results in mRNA decay and functional haploinsufficiency

inferredcites →https://doi.org/10.1093/hmg/ddu733openalex-snapshot

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

inferredcites →https://doi.org/10.1093/nar/gkg509openalex-snapshot

SIFT: predicting amino acid changes that affect protein function

inferredcites →https://doi.org/10.1093/nar/gkr407openalex-snapshot

Predicting the functional impact of protein mutations: application to cancer genomics

inferredcites →https://doi.org/10.1093/nar/gks743openalex-snapshot

Functional impact bias reveals cancer drivers

inferredcites →https://doi.org/10.1093/nar/gkv1222openalex-snapshot

ClinVar: public archive of interpretations of clinically relevant variants

inferredcites →https://doi.org/10.1093/nar/gkw1121openalex-snapshot

COSMIC: somatic cancer genetics at high-resolution

inferredcites →https://doi.org/10.1101/190330openalex-snapshot

The whole-genome panorama of cancer drivers

inferredcites →https://doi.org/10.1101/gad.1941710openalex-snapshot

The Mdm2–p53 relationship evolves: Mdm2 swings both ways as an oncogene and a tumor suppressor

inferredcites →https://doi.org/10.1101/gr.092619.109openalex-snapshot

Identification of deleterious mutations within three human genomes

inferredcites →https://doi.org/10.1101/gr.134635.111openalex-snapshot

MuSiC: Identifying mutational significance in cancer genomes

inferredcites →https://doi.org/10.1110/ps.03154503openalex-snapshot

A graph‐theory algorithm for rapid protein side‐chain prediction

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1126/science.1229259openalex-snapshot

Highly Recurrent TERT Promoter Mutations in Human Melanoma

inferredcites →https://doi.org/10.1126/science.1230062openalex-snapshot

TERT Promoter Mutations in Familial and Sporadic Melanoma

inferredcites →https://doi.org/10.1126/science.1235122openalex-snapshot

Cancer Genome Landscapes

inferredcites →https://doi.org/10.1126/science.aaa9119openalex-snapshot

The origins, determinants, and consequences of human mutations

inferredcites →https://doi.org/10.1126/science.aab4082openalex-snapshot

Somatic mutation in cancer and normal cells

inferredcites →https://doi.org/10.1158/0008-5472.can-06-1736openalex-snapshot

Distinguishing Cancer-Associated Missense Mutations from Common Polymorphisms

inferredcites →https://doi.org/10.1158/0008-5472.can-09-1133openalex-snapshot

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

inferredcites →https://doi.org/10.1186/1471-2164-10-s1-s12openalex-snapshot

Protein disorder in the human diseasome: unfoldomics of human genetic diseases

inferredcites →https://doi.org/10.1186/1471-2164-14-3openalex-snapshot

Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses

inferredcites →https://doi.org/10.1186/1471-2164-14-s1-s7openalex-snapshot

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

inferredcites →https://doi.org/10.1186/1471-2164-14-s3-s3openalex-snapshot

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

inferredcites →https://doi.org/10.1186/1471-2164-14-s3-s7openalex-snapshot

Assessment of computational methods for predicting the effects of missense mutations in human cancers

inferredcites →https://doi.org/10.1186/1471-2164-9-s1-s1openalex-snapshot

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

inferredcites →https://doi.org/10.1186/1471-2164-9-s2-s1openalex-snapshot

The unfoldomics decade: an update on intrinsically disordered proteins

inferredcites →https://doi.org/10.1186/gb-2011-12-4-r41openalex-snapshot

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

inferredcites →https://doi.org/10.1186/gm13openalex-snapshot

The Human Gene Mutation Database: 2008 update

inferredcites →https://doi.org/10.1186/gm390openalex-snapshot

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

inferredcites →https://doi.org/10.1186/s13059-014-0484-1openalex-snapshot

Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations

inferredcites →https://doi.org/10.1186/s13073-018-0531-8openalex-snapshot

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

inferredcites →https://doi.org/10.1371/journal.pcbi.1000601openalex-snapshot

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

inferredcites →https://doi.org/10.1371/journal.pcbi.1002709openalex-snapshot

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

inferredcites →https://doi.org/10.1371/journal.pgen.1000888openalex-snapshot

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

inferredcites →https://doi.org/10.1371/journal.pone.0046688openalex-snapshot

Predicting the Functional Effect of Amino Acid Substitutions and Indels

inferredcites →https://doi.org/10.1371/journal.pone.0066273openalex-snapshot

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

inferredcites →https://doi.org/10.1371/journal.pone.0077945openalex-snapshot

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

inferredcites →https://doi.org/10.17615/hvp3-wg08openalex-snapshot

Integrated genomic analyses of ovarian carcinoma

What points at this work

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

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PRKN-linked familial Parkinson’s disease: cellular and molecular mechanisms of disease-linked variants

inferred← citeshttps://doi.org/10.1016/j.str.2022.05.016openalex-snapshot

Disease-linked mutations cause exposure of a protein quality control degron

inferred← citeshttps://doi.org/10.1186/s40246-021-00371-yopenalex-snapshot

Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease

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