KDM5A p.Pro507=
c.1521A>G · VCV4534039
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -4.8 |
| Overall | ||
| CADD | 8.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,004 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,890 alleles · very rare
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
- KDM5A
- Protein
- p.Pro507=
- Coding
- c.1521A>G
- MANE Select
- NM_001042603
- Type
- single nucleotide variant
- Location
- chr12:333619 (GRCh38)
- Gene constraint
- LOEUF 0.27 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.98 · 46 PDB
- Residue 507
- the jmjc domain
Similar variants
- KDM5A c.4074+1G>A Likely pathogenic ★★ same type
- KDM5A p.Ala1260Val Uncertain significance ★★ ⚠ same type
- KDM5A p.Ala736Thr Uncertain significance ★★ ⚠ same type
- KDM5A p.Glu1021Gly Uncertain significance ★★ ⚠ same type
- KDM5A p.Gly630Glu Uncertain significance ★★ ⚠ same type
- KDM5A p.Ile1011Thr Uncertain significance ★★ ⚠ same type
- KDM5A p.Ser479Cys Uncertain significance ★★ ⚠ same type
- KDM5A p.Ser572Cys Uncertain significance ★★ ⚠ 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/kdm5a-p-pro507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown