Relevance of vep-lit-20261014-protocol-livesey2025-dms-indirect to use-case-rare-disease-candidate-ranking

Stable ID: use-case-mapping-vep-lit-20261014-rare-disease-candidate-ranking-livesey2025-dms-indirect

field

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

value

vep-lit-20261014-protocol-livesey2025-dms-indirect

relevance

proxy

endpoint

Average pairwise win rate by |Spearman| with the DMS assays the authors class as indirect

rationale

Proxy, as for the all-assay ranking; a robustness check on indirect (mostly growth) assays.

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

Which assays are indirect is not fully recoverable from Table S1.; Correlation is assessed within each protein, so the ranking does not test whether scores are comparable across genes; the authors report that DMS and clinical rankings agree closely for population-free and population-tuned VEPs (Pearson r 0.978 and 0.994) and less for clinical-trained VEPs (Results, Fig. 4).; 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 S5; Results

source locator

vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results

headline metric

pairwise-win-rate

comparison group

livesey-marsh-2025-vep-ranking

comparison title

Livesey and Marsh 2025 VEP rankings

stratum label

DMS benchmark, indirect assays only

stratum order

3

reason

VEP literature pass 2026-10-14: relevance of a newly extracted protocol (rewire-benchmark-data issues #153-#155).

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: 2026-10-14T15:30:00Z; method: ai-assisted-source-review; scope-review; method note: Checked the endpoint against the use case's question, inputs, exclusions and setting in data/entities/use-cases.jsonl; checked each limitation against the cited sources; listed every evaluation on the protocol in reviewed_evaluations after review/check_values.py matched its results.; note: Judgement drafted by the extraction agent and revised in review (docs/reviews/vep-literature-2026-10-14-review.md). Proxy is justified; see the dated review.

reviewed evaluations

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

pins

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• subject: Rank rare-disease variants for review