KDM4E p.Ala187=
c.561C>T · rs61740268 · VCV770403
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.68%, amr) — too common for a highly-penetrant pathogenic allele
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 -7.1 | GERP -3.8 |
| Overall | ||
| CADD | 0.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.68%
Admixed American · 5,403/55,808 alleles
Filtering AF
9.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.38%
Overall
2.48%
38,888/1,566,668 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 9.68% | 10 |
| East Asian | 5.46% | 18 |
| Ashkenazi Jewishnot grpmax-eligible | 4.64% | 22 |
| Amishnot grpmax-eligible | 3.3% | 30 |
| Remaining individualsnot grpmax-eligible | 2.84% | 35 |
| Middle Eastern | 2.68% | 37 |
| African / African-American | 2.43% | 41 |
| Finnishnot grpmax-eligible | 2.39% | 42 |
| South Asian | 2.08% | 48 |
| European (non-Finnish) | 1.98% | 50 |
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.Ala187=
- Coding
- c.561C>T
- MANE Select
- NM_001161630
- dbSNP
- rs61740268
- Type
- single nucleotide variant
- Location
- chr11:95026118 (GRCh38)
- Structure
- AlphaFold pLDDT 76.85 · 1 PDB
- Residue 187
- the jmjc domain; a β-strand
Similar variants
- 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
- KDM4E p.Arg100Cys 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-ala187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown