Evaluation

Phen2Gene default singleton on KMCGD 209

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Evaluation results

1 evaluation · 7 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	2.4% 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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 1(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	20.6% 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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 10(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	29.7% top-20-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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 20(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	36.4% top-30-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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 30(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	40.7% top-40-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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 40(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	13.4% top-5-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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 5(%)'
Configuration: Phen2Gene default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	43.5% top-50-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 Phen2Gene default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 21 (KMCGD, Phen2Gene), column 'TOP 50(%)'

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

Evaluation procedure

rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default

Configuration: Phen2Gene default, singleton (Yuan et al. 2022)
Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3)
Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
dataset version: As selected by Yuan et al.
split: No split
population: 209 solved in-house cases
inputs: Proband HPO terms only; singleton
adaptation: Default parameters
metric implementation: Rank of the causal gene per case
aggregation: Percentage of cases
budget: Top 1 to top 50 genes
protocol id: rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split
Adaptation: Default parameters
Scoring implementation: Rank of the causal gene per case

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Evidence

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Evidence table

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36 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
attributes.comparison.adaptation Default parameters Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Default parameters Context-only references	Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 Retrieved: 2026-10-09T21:18:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707` Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Inspected artifact
attributes.comparison.aggregation Percentage of cases Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Percentage of cases Context-only references	Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 Retrieved: 2026-10-09T21:18:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707` Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Inspected artifact
attributes.comparison.budget Top 1 to top 50 genes Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Top 1 to top 50 genes Context-only references	Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 Retrieved: 2026-10-09T21:18:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707` Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Inspected artifact
attributes.comparison.dataset_version As selected by Yuan et al. Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version As selected by Yuan et al. Context-only references	Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 Retrieved: 2026-10-09T21:18:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707` Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Inspected artifact
attributes.comparison.inputs Proband HPO terms only; singleton Context-only references	Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML Retrieved: 2026-10-09T21:18:05Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `a0e15e5a113ecbc1c8a3b17072a4028c55ae53c09ba0677d6fdb7601cfc8f1ca` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Proband HPO terms only; singleton Context-only references	Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) Original source ↗ SM Table 3 rows 'KMCGD', method 'Phen2Gene' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623 Retrieved: 2026-10-09T21:18:19Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `5a49ff00fe9b6ed8a92786c83cee79da7b2c9b958a6784d41e496ef59f17e707` Hash scope: SHA-256 of the docx member (zip SHA-256 2477ed033ada78ae776a159b0cf0a0daa15231a71a6f87ea705e6e4d3d996d41; assembled per request). Inspected artifact

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Sources and history

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

2 source records and release history

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases · Original source · Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML
Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · Original source · sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-eval-yuan2022-kmcgd-phen2gene

areas: dna-genomes
contexts: clinical_research
origin: independent_paper
protocol: rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default
version: Primary source as retrieved 2026-10-09
comparison: dataset version: As selected by Yuan et al.; split: No split; population: 209 solved in-house cases; inputs: Proband HPO terms only; singleton; adaptation: Default parameters; metric implementation: Rank of the causal gene per case; aggregation: Percentage of cases; budget: Top 1 to top 50 genes; protocol id: rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default
source locator: SM Table 3 rows 'KMCGD', method 'Phen2Gene'

Related records

system: Phen2Gene default, singleton (Yuan et al. 2022)
assessment: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3)
data: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)
evaluation: yuan2022-kmcgd-phen2gene-top1 top-1-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top10 top-10-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top20 top-20-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top30 top-30-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top40 top-40-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top5 top-5-accuracy
evaluation: yuan2022-kmcgd-phen2gene-top50 top-50-accuracy

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