KAT5 p.Pro7Ser
c.19C>T · VCV4858585
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00276%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.08 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.7 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 544 bp · p 0.75 · regional, not allelic |
| Overall | ||
| CADD | 24.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00276%
East Asian · 1/36,222 alleles
Overall
0.000139%
2/1,437,284 alleles · very rare
exomes 2/1,285,026 · genomes 0/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00276% | 36,222 |
| South Asian | 0.00152% | 65,618 |
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.Pro7Ser
- Coding
- c.19C>T
- MANE Select
- NM_182710
- Type
- single nucleotide variant
- Location
- chr11:65712286 (GRCh38)
- Gene constraint
- LOEUF 0.594 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 76.76 · 3 PDB
Similar variants
- KAT5 p.Pro7Ala Uncertain significance ★ same residue
- KAT5 p.Pro7Leu Uncertain significance ★ same residue
- 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
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-pro7ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown