KDM5C p.Pro531=
c.1593G>A · rs782494226 · VCV2660595
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00346%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -5.7 |
| Overall | ||
| CADD | 0.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00346%
African / African-American · 2/57,813 alleles
Filtering AF
0.000574%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000215%
Overall
0.000546%
6/1,098,170 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00346% | 28,906 |
| East Asian | 0.00295% | 33,855 |
| South Asian | 0.00175% | 56,993 |
| European (non-Finnish) | 0.000223% | 447,776 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- KDM5C
- Protein
- p.Pro531=
- Coding
- c.1593G>A
- MANE Select
- NM_004187
- dbSNP
- rs782494226
- Type
- single nucleotide variant
- Location
- chrX:53210567 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 531
- the jmjc domain
Similar variants
- KDM5C p.Pro531Leu Pathogenic/Likely pathogenic ★★ same residue
- KDM5C c.1243-2A>G Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg332Ter Pathogenic ★★ same type
- KDM5C p.Arg599Cys Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg681Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg68Ter Pathogenic ★★ same type
- KDM5C p.Arg750Trp Likely pathogenic ★★ same type
- KDM5C p.Arg778Ter Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/kdm5c-p-pro531 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown