KAT8 p.Gln4=
c.12G>A · VCV4929576
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.813%, 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 1.6 | GERP -0.029, phastCons 1 |
| Overall | ||
| CADD | 8.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.813%
African / African-American · 536/65,924 alleles
Filtering AF
0.756%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.734%
Overall
0.0426%
596/1,397,796 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.813% | 123 |
| Middle Eastern | 0.0883% | 1,132 |
| Admixed American | 0.0556% | 1,799 |
| Remaining individualsnot grpmax-eligible | 0.0551% | 1,816 |
| European (non-Finnish) | 0.00103% | 97,371 |
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
- KAT8
- Protein
- p.Gln4=
- Coding
- c.12G>A
- MANE Select
- NM_032188
- Type
- single nucleotide variant
- Location
- chr16:31117693 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 44 PDB
- Residue 4
- the 'disordered' region
Similar variants
- KAT8 p.Gln4His Uncertain significance ★ ⚠ same residue
- KAT8 p.Tyr90Cys Likely pathogenic ★★ same type
- KAT8 p.Arg144His Uncertain significance ★★ ⚠ same type
- KAT8 p.Gly19Arg Uncertain significance ★★ ⚠ same type
- KAT8 p.Ile57Val Uncertain significance ★★ ⚠ same type
- KAT8 p.Lys203Ter Uncertain significance ★★ same type
- KAT8 p.Leu370= Benign ★★ same type
- KAT8 p.Pro352= Benign ★★ 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/kat8-p-gln4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown