KAT6A p.Val829=
c.2487A>G · rs10104089 · VCV587953
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.64%, afr)
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 0.67 | GERP -1, phastCons 0.99 |
| Overall | ||
| CADD | 7.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.64%
African / African-American · 1,229/75,004 alleles
Filtering AF
1.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.53%
Overall
0.0867%
1,396/1,609,668 alleles · low-frequency
exomes 678/1,457,334 · genomes 718/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.64% | 61 |
| Admixed American | 0.122% | 821 |
| Remaining individualsnot grpmax-eligible | 0.11% | 905 |
| Middle Eastern | 0.0991% | 1,009 |
| European (non-Finnish) | 0.00153% | 65,544 |
| South Asian | 0.0011% | 90,986 |
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.Val829=
- Coding
- c.2487A>G
- MANE Select
- NM_006766
- dbSNP
- rs10104089
- Type
- single nucleotide variant
- Location
- chr8:41941394 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 829
- the 'disordered' region
Similar variants
- KAT6A p.Val829Ala 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-val829 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown