KAT5 p.Val32Asp
c.95T>A · rs146788368 · VCV2636040
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.104%, mid)
Conditions
1
KAT5-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.7 | GERP 0.4, phastCons 1 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 544 bp · p 0.75 · regional, not allelic |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
Middle Eastern · 6/5,794 alleles
Filtering AF
0.045%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0308%
Overall
0.00357%
55/1,541,532 alleles · rare
exomes 52/1,389,588 · genomes 3/151,944 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.104% | 966 |
| Remaining individualsnot grpmax-eligible | 0.00676% | 14,783 |
| European (non-Finnish) | 0.0039% | 25,658 |
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
- KAT5
- Protein
- p.Val32Asp
- Coding
- c.95T>A
- MANE Select
- NM_182710
- dbSNP
- rs146788368
- Type
- single nucleotide variant
- Location
- chr11:65712362 (GRCh38)
- Gene constraint
- LOEUF 0.594 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 76.76 · 3 PDB
- Residue 32
- the tudor-knot domain; a β-strand
Disease context
KAT5-related disorder
Similar variants
- KAT5 p.Arg219Gln Uncertain significance ★ ⚠ same condition
- KAT5 p.Thr395Ala Uncertain significance ⚠ same condition
- KAT5 c.615+7T>A Likely benign same condition
- KAT5 p.Cys308Ser Uncertain significance ★★ same type
- KAT5 p.Gln310His Uncertain significance ★★ ⚠ same type
- KAT5 p.Ser223Leu Uncertain significance ★★ ⚠ same type
- KAT5 p.Thr180Met Uncertain significance ★★ ⚠ same type
- KAT5 p.Gly43= Benign/Likely 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/kat5-p-val32asp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown