KAT6A p.Arg313=
c.939G>A · rs752218810 · VCV2100914
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000848%, nfe)
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 2.2 | GERP -0.36, phastCons 1 |
| Overall | ||
| CADD | 10.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000848%
European (non-Finnish) · 10/1,179,718 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.00062%
10/1,613,470 alleles · very rare
exomes 10/1,461,430 · genomes 0/152,040 · joint denominator
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.Arg313=
- Coding
- c.939G>A
- MANE Select
- NM_006766
- dbSNP
- rs752218810
- Type
- single nucleotide variant
- Location
- chr8:41978746 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 313
- the 'interaction with runx1-1' region; an α-helix; 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-arg313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown