KAT5 p.Ile513=
c.1539C>T · VCV4084139
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0683%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.034 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.25 | phastCons 0.19 |
| Overall | ||
| CADD | 9.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0683%
Admixed American · 41/59,990 alleles
Filtering AF
0.0518%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0459%
Overall
0.00397%
64/1,614,044 alleles · ultra-rare
exomes 47/1,461,822 · genomes 17/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0683% | 1,463 |
| African / African-American | 0.00267% | 37,465 |
| East Asian | 0.00223% | 44,896 |
| European (non-Finnish) | 0.00169% | 59,002 |
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.Ile513=
- Coding
- c.1539C>T
- MANE Select
- NM_182710
- Type
- single nucleotide variant
- Location
- chr11:65719079 (GRCh38)
- Gene constraint
- LOEUF 0.594 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 76.76 · 3 PDB
- Residue 513
- the 'interaction with atf2' 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-ile513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown