Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.3%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.147 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.26 | phastCons 0.2 |
| Overall | ||
| CADD | 9.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.3%
African / African-American · 4,723/74,966 alleles
Filtering AF
6.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.09%
Overall
0.322%
5,191/1,613,992 alleles · common
exomes 2,528/1,461,860 · genomes 2,663/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.3% | 16 |
| Remaining individualsnot grpmax-eligible | 0.336% | 298 |
| Admixed American | 0.278% | 359 |
| Middle Eastern | 0.116% | 864 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.00653% | 15,325 |
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.Ser66=
- Coding
- c.198C>T
- MANE Select
- NM_182710
- dbSNP
- rs4645914
- Type
- single nucleotide variant
- Location
- chr11:65712785 (GRCh38)
- Gene constraint
- LOEUF 0.594 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 76.76 · 3 PDB
- Residue 66
- an α-helix
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.Thr432= Likely benign ★★ same type
- RNASEH2C c.*1007C>G 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-ser66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown