KAT6A p.Arg442=
c.1326G>A · rs143853582 · VCV2070083
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0427%, afr)
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 4.1 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 12.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0427%
African / African-American · 32/74,932 alleles
Filtering AF
0.031%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.00267%
43/1,611,822 alleles · ultra-rare
exomes 15/1,459,540 · genomes 28/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0427% | 2,342 |
| Admixed American | 0.00836% | 11,964 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,592 |
| European (non-Finnish) | 0.00017% | 589,244 |
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.Arg442=
- Coding
- c.1326G>A
- MANE Select
- NM_006766
- dbSNP
- rs143853582
- Type
- single nucleotide variant
- Location
- chr8:41977045 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 442
- the 'interaction with runx1-1' region; the 'disordered' region; the 'interaction with pml' region
Similar variants
- 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
- KAT6A p.Arg251Ter 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-arg442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown