KAT6A p.Asp930=
c.2790C>T · rs142510204 · VCV1897035
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, sas)
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 -1.8 | GERP -4.9 |
| Overall | ||
| CADD | 0.541 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,076 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00427%
69/1,614,178 alleles · ultra-rare
exomes 61/1,461,892 · genomes 8/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,554 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,628 |
| European (non-Finnish) | 0.00356% | 28,096 |
| African / African-American | 0.00267% | 37,516 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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.Asp930=
- Coding
- c.2790C>T
- MANE Select
- NM_006766
- dbSNP
- rs142510204
- Type
- single nucleotide variant
- Location
- chr8:41941091 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 930
- the 'disordered' region
Similar variants
- KAT6A p.Asp930Glu Likely benign ★★ same residue
- KAT6A c.3353-1G>A Pathogenic/Likely pathogenic ★★ same type
- KAT6A p.Arg1012Ter Pathogenic ★★ same type
- KAT6A p.Arg1019Ter Pathogenic/Likely pathogenic ★★ same type
- KAT6A p.Arg1024Ter Pathogenic ★★ same type
- KAT6A p.Arg1129Ter Pathogenic ★★ same type
- KAT6A p.Arg148Ter Pathogenic ★★ same type
- KAT6A p.Arg220Ter Pathogenic/Likely pathogenic ★★ 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/kat6a-p-asp930 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown