KAT6A p.Pro1652=
c.4956A>G · rs201475966 · VCV589069
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0955%, nfe)
Conditions
1
Inborn genetic diseases
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 -20 | GERP -5.5 |
| Overall | ||
| CADD | 0.038 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0955%
European (non-Finnish) · 1,100/1,152,172 alleles
Filtering AF
0.0907%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0888%
Overall
0.0754%
1,171/1,552,318 alleles · ultra-rare
exomes 1,103/1,400,928 · genomes 68/151,390 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0955% | 1,047 |
| Remaining individualsnot grpmax-eligible | 0.0678% | 1,475 |
| Finnishnot grpmax-eligible | 0.0284% | 3,521 |
| African / African-American | 0.0162% | 6,168 |
| East Asian | 0.00465% | 21,525 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0036% | 27,764 |
| Admixed American | 0.00181% | 55,220 |
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
- KAT6A
- Protein
- p.Pro1652=
- Coding
- c.4956A>G
- MANE Select
- NM_006766
- dbSNP
- rs201475966
- Type
- single nucleotide variant
- Location
- chr8:41933264 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 1652
- the 'interaction with pml' region; the 'disordered' region
Similar variants
- KAT6A p.Pro1652_Pro1659del Benign/Likely benign ★★ same residue
- KAT6A p.Arg1129Ter Pathogenic ★★ same condition
- KAT6A p.Arg148Ter Pathogenic ★★ same condition
- KAT6A p.Arg286Ter Pathogenic ★★ same condition
- KAT6A p.Arg735Ter Pathogenic ★★ same condition
- KAT6A p.Ala1451Gly Uncertain significance ★★ ⚠ same condition
- KAT6A p.Ala492Val Uncertain significance ★★ ⚠ same condition
- KAT6A p.Arg1086Ser Uncertain significance ★★ ⚠ same condition
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/kat6a-p-pro1652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown