KDM4E p.Pro495=
c.1485G>A · rs61737594 · VCV740794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.125%, 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 -0.52 | GERP -3.1 |
| Overall | ||
| CADD | 0.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.125%
African / African-American · 91/73,084 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0961%
Overall
0.00755%
116/1,537,066 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.125% | 803 |
| Middle Eastern | 0.0167% | 5,990 |
| Remaining individualsnot grpmax-eligible | 0.01% | 10,004 |
| Admixed American | 0.00588% | 16,998 |
| South Asian | 0.00476% | 21,012 |
| European (non-Finnish) | 0.000959% | 104,259 |
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
- KDM4E
- Protein
- p.Pro495=
- Coding
- c.1485G>A
- MANE Select
- NM_001161630
- dbSNP
- rs61737594
- Type
- single nucleotide variant
- Location
- chr11:95027042 (GRCh38)
- Structure
- AlphaFold pLDDT 76.85 · 1 PDB
Similar variants
- KDM4E p.Ala187= Likely benign ★★ same type
- KDM4E p.Cys381Tyr Benign ★★ same type
- KDM4E p.Gln42Arg Benign ★★ same type
- KDM4E p.Thr190= Likely benign ★★ same type
- KDM4E p.Ala224Asp Uncertain significance ★ ⚠ same type
- KDM4E p.Ala265Val Uncertain significance ★ ⚠ same type
- KDM4E p.Ala287Thr Uncertain significance ★ same type
- KDM4E p.Ala406Thr 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/kdm4e-p-pro495 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown