KAT2A p.Glu780=
c.2340G>A · rs377452807 · VCV2647782
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.187%, sas)
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 0.6 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 5.765 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.187%
South Asian · 168/89,670 alleles
Filtering AF
0.164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.155%
Overall
0.0153%
245/1,598,554 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.187% | 534 |
| East Asian | 0.083% | 1,204 |
| Remaining individualsnot grpmax-eligible | 0.0583% | 1,715 |
| African / African-American | 0.00271% | 36,904 |
| European (non-Finnish) | 0.00017% | 587,137 |
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
- KAT2A
- Protein
- p.Glu780=
- Coding
- c.2340G>A
- MANE Select
- NM_021078
- dbSNP
- rs377452807
- Type
- single nucleotide variant
- Location
- chr17:42113823 (GRCh38)
- Gene constraint
- LOEUF 0.587 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.62 · 15 PDB
- Residue 780
- the bromo domain; an α-helix
Similar variants
- KAT2A c.464-18C>G Benign ★★ same type
- KAT2A p.Leu664= Benign ★★ same type
- KAT2A p.Leu719= Benign ★★ same type
- KAT2A p.Ala274Val Uncertain significance ★ ⚠ same type
- KAT2A p.Ala426Val Uncertain significance ★ ⚠ same type
- KAT2A p.Ala53Ser Uncertain significance ★ ⚠ same type
- KAT2A p.Ala53Val Uncertain significance ★ ⚠ same type
- KAT2A p.Arg171Gly Uncertain significance ★ ⚠ 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/kat2a-p-glu780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown