KAT5 p.Ser201=
c.603G>A · VCV4847128
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.197 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.2 | |
| Overall | ||
| CADD | 2.016 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,890 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000558%
9/1,614,032 alleles · very rare
exomes 7/1,461,890 · genomes 2/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,445 |
| Admixed American | 0.00167% | 59,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| African / African-American | 0.00133% | 74,910 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000254% | 393,345 |
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.Ser201=
- Coding
- c.603G>A
- MANE Select
- NM_182710
- Type
- single nucleotide variant
- Location
- chr11:65713655 (GRCh38)
- Gene constraint
- LOEUF 0.594 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 76.76 · 3 PDB
- Residue 201
- the 'disordered' region
Similar variants
- 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.Val32Asp Uncertain significance ★★ same type
- KAT5 p.Gly43= Benign/Likely benign ★★ same type
- KAT5 p.Ser66= Benign ★★ same type
- KAT5 p.Thr432= 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-ser201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown