KDM4A p.Pro10=
c.30C>T · rs140577325 · VCV732098
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.36%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 12.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.36%
African / African-American · 1,768/74,990 alleles
Filtering AF
2.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.23%
Overall
0.121%
1,948/1,612,924 alleles · low-frequency
exomes 910/1,460,652 · genomes 1,038/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.36% | 42 |
| Remaining individualsnot grpmax-eligible | 0.154% | 651 |
| Admixed American | 0.0868% | 1,152 |
| European (non-Finnish) | 0.00254% | 39,313 |
| South Asian | 0.0022% | 45,399 |
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
- KDM4A
- Protein
- p.Pro10=
- Coding
- c.30C>T
- MANE Select
- NM_014663
- dbSNP
- rs140577325
- Type
- single nucleotide variant
- Location
- chr1:43653205 (GRCh38)
- Gene constraint
- LOEUF 0.258 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.49 · 89 PDB
- Residue 10
- an α-helix
Similar variants
- KDM4A c.2961+10G>A Benign ★★ same type
- KDM4A p.Ala493= Benign ★★ same type
- KDM4A p.Met374Val Benign ★★ same type
- KDM4A p.Thr16= Benign ★★ same type
- KDM4A p.Thr76= Benign ★★ same type
- KDM4A p.Ala567Thr Uncertain significance ★ ⚠ same type
- KDM4A p.Ala577Thr Uncertain significance ★ ⚠ same type
- KDM4A p.Ala892Val 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/kdm4a-p-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown