ACAT1 p.Pro63=
c.189A>C · rs2496581644 · VCV2843573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
beta-ketothiolase deficiency
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 0.97 | GERP -4.8, phastCons 0.99 |
| Overall | ||
| CADD | 8.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ACAT1
- Protein
- p.Pro63=
- Coding
- c.189A>C
- MANE Select
- NM_003101 · reported on NM_000019
- dbSNP
- rs2496581644
- Type
- single nucleotide variant
- Location
- chr11:108133888 (GRCh38)
- Structure
- AlphaFold pLDDT 81.22 · 5 PDB
Disease context
beta-ketothiolase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Beta-ketothiolase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- ACAT1 c.1006-1G>A Pathogenic ★★ same condition
- ACAT1 c.1006-1G>C Pathogenic ★★ same condition
- ACAT1 c.1006-2A>C Pathogenic ★★ same condition
- ACAT1 c.1163+2T>C Pathogenic ★★ same condition
- ACAT1 c.120+1G>C Likely pathogenic ★★ same condition
- ACAT1 c.121-3C>G Pathogenic/Likely pathogenic ★★ same condition
- ACAT1 c.238+2T>A Pathogenic/Likely pathogenic ★★ same condition
- ACAT1 c.435+1G>A Pathogenic ★★ same condition
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/acat1-p-pro63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown