Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv to use-case-protein-variant-effect-prediction

Stable ID: use-case-mapping-vep-uc-20261014-protein-variant-effect-prediction-livesey2025-dms-snv

field

links:assessed_by:vep-lit-20261014-protocol-livesey2025-dms-snv

value

vep-lit-20261014-protocol-livesey2025-dms-snv

relevance

direct

endpoint

Average pairwise win rate by |Spearman| restricted to substitutions reachable by one nucleotide change

rationale

Direct: ranks 97 predictors by agreement with DMS measurements of human proteins, with ClinVar and gnomAD variants removed from the DMS sets, which is the comparison the use case needs; limited to human proteins.

constraints

Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results.; Compare rows only within this protocol.

limitations

Human proteins only (36 DMS sets, one per protein).; Five VEPs were trained on DMS data (Envision, CPT-1, DeMaSk, VARITY_R, VARITY_ER); the authors excluded their results for the proteins used to train them (Table S2), but other methods may have been tuned against DMS data without direct training, for example ESM-1v's model selection (Results, Discussion).; Per-protein correlations are in the figshare deposit, not retrieved; averages do not predict a single protein.; Transcribed from the source; no reproduction by Rewire and no human scientific review.

citation locators

source id: vep-lit-20261014-source-livesey2025-supplementary-2; locator: Supplementary Material 2 Table S6; Results; source id: vep-lit-20261014-source-livesey2025-article; locator: Methods 'DMS datasets'

source locator

vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S6; Results; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets'

headline metric

pairwise-win-rate

comparison group

livesey-marsh-2025-vep-ranking

comparison title

Livesey and Marsh 2025 VEP rankings

stratum label

DMS benchmark, SNV-accessible substitutions

stratum order

4

reason

VEP use-case pass 2026-10-14: relevance of a protocol to a new use case (rewire-benchmark-data #151/#152).

review

reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T16:00:00Z; method: ai-assisted-source-review; scope-review; method note: Checked the endpoint against the use case's question, inputs, exclusions and output; checked each limitation and number against the cited sources, re-downloaded and hash-matched; listed every evaluation on the protocol in reviewed_evaluations (values of evaluations already in the store were checked by their own independent reviews).; note: Judgement drafted by the extraction agent and revised in review (docs/reviews/vep-use-cases-2026-10-14-review.md).

reviewed evaluations

vep-lit-20261014-eval-livesey2025-dms-snv-3cnet; vep-lit-20261014-eval-livesey2025-dms-snv-alphamissense; vep-lit-20261014-eval-livesey2025-dms-snv-alphscore; vep-lit-20261014-eval-livesey2025-dms-snv-bayesdel; vep-lit-20261014-eval-livesey2025-dms-snv-bayesdel-noaf; vep-lit-20261014-eval-livesey2025-dms-snv-blosum62; vep-lit-20261014-eval-livesey2025-dms-snv-cadd-1-6; vep-lit-20261014-eval-livesey2025-dms-snv-cadd-1-7; vep-lit-20261014-eval-livesey2025-dms-snv-capice; vep-lit-20261014-eval-livesey2025-dms-snv-carp; vep-lit-20261014-eval-livesey2025-dms-snv-clinpred; vep-lit-20261014-eval-livesey2025-dms-snv-condel; vep-lit-20261014-eval-livesey2025-dms-snv-cpt-1; vep-lit-20261014-eval-livesey2025-dms-snv-dann; vep-lit-20261014-eval-livesey2025-dms-snv-deepsav; vep-lit-20261014-eval-livesey2025-dms-snv-deepsequence; vep-lit-20261014-eval-livesey2025-dms-snv-demask; vep-lit-20261014-eval-livesey2025-dms-snv-deogen2; vep-lit-20261014-eval-livesey2025-dms-snv-eigen; vep-lit-20261014-eval-livesey2025-dms-snv-envision; vep-lit-20261014-eval-livesey2025-dms-snv-escott; vep-lit-20261014-eval-livesey2025-dms-snv-esm-1b; vep-lit-20261014-eval-livesey2025-dms-snv-esm-1v; vep-lit-20261014-eval-livesey2025-dms-snv-esm2; vep-lit-20261014-eval-livesey2025-dms-snv-eve; vep-lit-20261014-eval-livesey2025-dms-snv-evmutation-epistatic; vep-lit-20261014-eval-livesey2025-dms-snv-evmutation-independent; vep-lit-20261014-eval-livesey2025-dms-snv-fathmm; vep-lit-20261014-eval-livesey2025-dms-snv-fathmm-mkl; vep-lit-20261014-eval-livesey2025-dms-snv-fathmm-xf; vep-lit-20261014-eval-livesey2025-dms-snv-fitcons; vep-lit-20261014-eval-livesey2025-dms-snv-gemme; vep-lit-20261014-eval-livesey2025-dms-snv-genocanyon; vep-lit-20261014-eval-livesey2025-dms-snv-gerp-plus-plus; vep-lit-20261014-eval-livesey2025-dms-snv-gmvp; vep-lit-20261014-eval-livesey2025-dms-snv-grantham; vep-lit-20261014-eval-livesey2025-dms-snv-igemme; vep-lit-20261014-eval-livesey2025-dms-snv-inmerf; vep-lit-20261014-eval-livesey2025-dms-snv-lassie; vep-lit-20261014-eval-livesey2025-dms-snv-list-s2; vep-lit-20261014-eval-livesey2025-dms-snv-lrt; vep-lit-20261014-eval-livesey2025-dms-snv-m-cap; vep-lit-20261014-eval-livesey2025-dms-snv-maverick-benign; vep-lit-20261014-eval-livesey2025-dms-snv-metalr; vep-lit-20261014-eval-livesey2025-dms-snv-metarnn; vep-lit-20261014-eval-livesey2025-dms-snv-metasvm; vep-lit-20261014-eval-livesey2025-dms-snv-mistic; vep-lit-20261014-eval-livesey2025-dms-snv-moipred-benign; vep-lit-20261014-eval-livesey2025-dms-snv-mpc; vep-lit-20261014-eval-livesey2025-dms-snv-msa-transformer; vep-lit-20261014-eval-livesey2025-dms-snv-mutationassessor; vep-lit-20261014-eval-livesey2025-dms-snv-mutationtcn; vep-lit-20261014-eval-livesey2025-dms-snv-mutformer; vep-lit-20261014-eval-livesey2025-dms-snv-mutpred; vep-lit-20261014-eval-livesey2025-dms-snv-mutscore; vep-lit-20261014-eval-livesey2025-dms-snv-mvp; vep-lit-20261014-eval-livesey2025-dms-snv-mvppt; vep-lit-20261014-eval-livesey2025-dms-snv-panther; vep-lit-20261014-eval-livesey2025-dms-snv-phact; vep-lit-20261014-eval-livesey2025-dms-snv-phactboost; vep-lit-20261014-eval-livesey2025-dms-snv-phastcons; vep-lit-20261014-eval-livesey2025-dms-snv-phd-snp; vep-lit-20261014-eval-livesey2025-dms-snv-phd-snpg; vep-lit-20261014-eval-livesey2025-dms-snv-phylop; vep-lit-20261014-eval-livesey2025-dms-snv-polyphen2-humdiv; vep-lit-20261014-eval-livesey2025-dms-snv-polyphen2-humvar; vep-lit-20261014-eval-livesey2025-dms-snv-ponp2; vep-lit-20261014-eval-livesey2025-dms-snv-popeve; vep-lit-20261014-eval-livesey2025-dms-snv-primateai; vep-lit-20261014-eval-livesey2025-dms-snv-progen2; vep-lit-20261014-eval-livesey2025-dms-snv-protgpt2; vep-lit-20261014-eval-livesey2025-dms-snv-provean; vep-lit-20261014-eval-livesey2025-dms-snv-revel; vep-lit-20261014-eval-livesey2025-dms-snv-rhapsody; vep-lit-20261014-eval-livesey2025-dms-snv-rita; vep-lit-20261014-eval-livesey2025-dms-snv-saprot; vep-lit-20261014-eval-livesey2025-dms-snv-sequence-unet; vep-lit-20261014-eval-livesey2025-dms-snv-sift; vep-lit-20261014-eval-livesey2025-dms-snv-sift4g; vep-lit-20261014-eval-livesey2025-dms-snv-sigma; vep-lit-20261014-eval-livesey2025-dms-snv-siphy; vep-lit-20261014-eval-livesey2025-dms-snv-snap2; vep-lit-20261014-eval-livesey2025-dms-snv-snpred; vep-lit-20261014-eval-livesey2025-dms-snv-snps-and-go; vep-lit-20261014-eval-livesey2025-dms-snv-snps-and-go3d; vep-lit-20261014-eval-livesey2025-dms-snv-spri; vep-lit-20261014-eval-livesey2025-dms-snv-suspect; vep-lit-20261014-eval-livesey2025-dms-snv-trancepteve; vep-lit-20261014-eval-livesey2025-dms-snv-tranception; vep-lit-20261014-eval-livesey2025-dms-snv-uneecon; vep-lit-20261014-eval-livesey2025-dms-snv-unirep-evotune; vep-lit-20261014-eval-livesey2025-dms-snv-varity-er; vep-lit-20261014-eval-livesey2025-dms-snv-varity-r; vep-lit-20261014-eval-livesey2025-dms-snv-vespa; vep-lit-20261014-eval-livesey2025-dms-snv-vespal; vep-lit-20261014-eval-livesey2025-dms-snv-vest4; vep-lit-20261014-eval-livesey2025-dms-snv-wavenet

pins

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• subject: Predict missense variant effects in a protein of interest