KAT8 p.Thr60=
c.180G>T · VCV3378334
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.28e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.57 | donor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.4 | GERP -4.4, phastCons 0.008 |
| Overall | ||
| CADD | 9.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.28e-05%
European (non-Finnish) · 1/1,077,812 alleles
Overall
7.88e-05%
1/1,268,296 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.Thr60=
- Coding
- c.180G>T
- MANE Select
- NM_032188
- Type
- single nucleotide variant
- Location
- chr16:31117861 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 44 PDB
- Residue 60
- the tudor-knot domain
Similar variants
- KAT8 p.Thr60Ala 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-thr60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown