KDM5D
Chr Ylysine demethylase 5D
Also known as: HY, HYA, JARID1D, SMCY
The encoded protein is a histone demethylase that specifically removes methyl groups from lysine-4 of histone H3, playing a central role in gene expression regulation and transcriptional repression. KDM5D is located on the Y chromosome and follows Y-linked inheritance, meaning mutations are passed from fathers to sons only. The gene is highly constrained against loss-of-function variants, but specific disease associations have not been established in the provided data.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Tolerant to missense variation
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
125 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | — | — | — | — | 70 |
Likely Pathogenic | — | — | — | — | 2 |
VUS | — | — | — | — | 5 |
Likely Benign | — | — | — | — | 5 |
Benign | — | — | — | — | 0 |
| Total | — | 82 | |||
Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
KDM5D · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools