KDM3A p.Ile1069=
c.3207T>C · rs569604500 · VCV746373
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0417%, amr)
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 -0.048 | GERP -4.6, phastCons 0.87 |
| Overall | ||
| CADD | 9.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0417%
Admixed American · 25/60,014 alleles
Filtering AF
0.0289%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0247%
Overall
0.00161%
26/1,614,086 alleles · ultra-rare
exomes 14/1,461,762 · genomes 12/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0417% | 2,401 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
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
- KDM3A
- Protein
- p.Ile1069=
- Coding
- c.3207T>C
- MANE Select
- NM_018433
- dbSNP
- rs569604500
- Type
- single nucleotide variant
- Location
- chr2:86485753 (GRCh38)
- Gene constraint
- LOEUF 0.469 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 69.06
- Residue 1069
- the jmjc domain
Similar variants
- KDM3A c.2512+19T>C Benign ★★ same type
- KDM3A p.Leu1283= Benign/Likely benign ★★ same type
- KDM3A p.Leu937= Benign ★★ same type
- KDM3A p.Val63= Likely benign ★★ same type
- KDM3A c.1940-2A>G Uncertain significance ★ same type
- KDM3A p.Ala307Thr Uncertain significance ★ ⚠ same type
- KDM3A p.Ala322Thr Uncertain significance ★ ⚠ same type
- KDM3A p.Ala409Val 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/kdm3a-p-ile1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown