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

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

field

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

value

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

relevance

direct

endpoint

Average pairwise win rate by |Spearman| on SNV-accessible substitutions with missing predictions set to each VEP's most benign score

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 S7; 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 S7; 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, gaps filled

stratum order

5

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

pins

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