Configuration

Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)

Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) as evaluated in the cited comparison.

Overview

Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) as evaluated in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

2 evaluations · 40 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.766 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.93 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	82% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	85% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.799 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.938 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'ROC AUC', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	84% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@1 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	91% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@10 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.889 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'AUPR', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.967 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'ROC AUC', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	89% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@1 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	100% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@10 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.789 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'AUPR', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.936 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'ROC AUC', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	84% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@1 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	91% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@10 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.771 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'AUPR', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.932 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'ROC AUC', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	82% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@1 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	86% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@10 (%)', column 'ClinVar' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.445 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'PAVS' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.87 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'PAVS' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	58.6% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'PAVS' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	78.4% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'PAVS' 'Exomiser'
Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.618 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser on PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'PAVS' 'Exomiser'

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

1 source records and release history

The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Original source · Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-kafkas2025-exomiser-12-1-0

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025)
foundation model eligible: false
version: 12.1.0
parameters: Weighted combination of ExomeWalker, PHIVE and PhenIX gene scores; a random variant generated in each candidate gene; variant scores ignored; default settings
source locator: Methods 'Baseline methods'

Related records

configuration of: Exomiser
system: Exomiser on ClinVar candidate gene sets
system: Exomiser on PAVS candidate gene sets

Suggest a correction