KAT6A p.Pro1683=
c.5049G>A · rs759107686 · VCV2082599
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00564%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.6 | GERP -4.8 |
| Overall | ||
| CADD | 2.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00564%
European (non-Finnish) · 66/1,169,704 alleles
Filtering AF
0.00455%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00415%
Overall
0.00459%
73/1,591,982 alleles · very rare
exomes 73/1,440,396 · genomes 0/151,586 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00564% | 17,723 |
| Admixed American | 0.00342% | 29,235 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,882 |
| East Asian | 0.00225% | 44,480 |
| African / African-American | 0.00134% | 74,616 |
| South Asian | 0.00111% | 89,754 |
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
- KAT6A
- Protein
- p.Pro1683=
- Coding
- c.5049G>A
- MANE Select
- NM_006766
- dbSNP
- rs759107686
- Type
- single nucleotide variant
- Location
- chr8:41933171 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 1683
- the 'interaction with pml' region; the 'disordered' region
Similar variants
- KAT6A p.Pro1683Leu Likely benign ★ ⚠ same residue
- KAT6A p.Pro1683fs Likely pathogenic ★ same residue
- KAT6A c.3353-1G>A Pathogenic/Likely pathogenic ★★ same type
- KAT6A p.Arg1012Ter Pathogenic ★★ same type
- KAT6A p.Arg1019Ter Pathogenic/Likely pathogenic ★★ same type
- KAT6A p.Arg1024Ter Pathogenic ★★ same type
- KAT6A p.Arg1129Ter Pathogenic ★★ same type
- KAT6A p.Arg148Ter Pathogenic ★★ 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/kat6a-p-pro1683 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown