KAT8 p.Pro235=
c.705C>G · VCV4681935
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -1.4 | GERP -5 |
| Overall | ||
| CADD | 7.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,028 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00041%
6/1,461,672 alleles · very rare
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
- KAT8
- Protein
- p.Pro235=
- Coding
- c.705C>G
- MANE Select
- NM_032188
- Type
- single nucleotide variant
- Location
- chr16:31128073 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 44 PDB
- Residue 235
- the myst-type hat domain; a UniProt-annotated variant site (found in a severe neurodevelopmental disorder similar to li-ghorbani-weisz-hubshman syndrome with apparently autosomal recessive inheritance; uncertain significance; loss of protein expression); the 'sufficient for interaction with kansl1' region
Similar variants
- KAT8 p.Pro235Arg Uncertain significance ★ ⚠ same residue
- KAT8 p.Tyr90Cys Likely pathogenic ★★ same type
- KAT8 p.Arg144His Uncertain significance ★★ ⚠ same type
- KAT8 p.Gly19Arg Uncertain significance ★★ ⚠ same type
- KAT8 p.Ile57Val Uncertain significance ★★ ⚠ same type
- KAT8 p.Lys203Ter Uncertain significance ★★ same type
- KAT8 p.Leu370= Benign ★★ same type
- KAT8 p.Pro352= 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/kat8-p-pro235 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown