KAT6A p.Phe615fs
c.1842_1846del · VCV4874881
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- KAT6A
- Protein
- p.Phe615fs
- Coding
- c.1842_1846del
- MANE Select
- NM_006766
- Type
- Deletion
- Location
- chr8:41947807 (GRCh38)
- Gene constraint
- LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12 · 21 PDB
- Residue 615
- the 'interaction with runx1-1' region; a β-strand; the 'catalytic' region; the 'mediates interaction with brpf1, required for histone h3 acetyltransferase activity' region; the myst-type hat domain; the 'interaction with pml' region
Similar variants
- KAT6A p.Asp503fs Pathogenic ★★ same type
- KAT6A p.Val1347fs Pathogenic/Likely pathogenic ★★ same type
- KAT6A p.Arg961_Arg972del Uncertain significance ★★ same type
- KAT6A p.Lys1224_Glu1225del Uncertain significance ★★ same type
- KAT6A p.1677_1680QQPQ[1] Benign/Likely benign ★★ same type
- KAT6A p.Ala1252_Ala1255del Likely benign ★★ same type
- KAT6A p.Pro1652_Pro1659del Benign/Likely benign ★★ same type
- KAT6A c.1903-5_1903-2del 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-phe615fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown