ACAA1 p.Ser154=
c.462C>T · rs139044259 · VCV3052426
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.72%, afr)
Conditions
1
ACAA1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.312 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.77 | GERP 0.91, phastCons 0.16 |
| Overall | ||
| CADD | 9.559 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.72%
African / African-American · 540/75,032 alleles
Filtering AF
0.669%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.65%
Overall
0.0392%
632/1,614,000 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.72% | 139 |
| Admixed American | 0.0633% | 1,579 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,838 |
| Middle Eastern | 0.0495% | 2,021 |
| European (non-Finnish) | 0.00144% | 69,406 |
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
- ACAA1
- Protein
- p.Ser154=
- Coding
- c.462C>T
- MANE Select
- NM_001607
- dbSNP
- rs139044259
- Type
- single nucleotide variant
- Location
- chr3:38129373 (GRCh38)
- Gene constraint
- LOEUF 1.199 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.93 · 2 PDB
- Residue 154
- a turn
Disease context
ACAA1-related disorder
Similar variants
- ACAA1 c.546-4C>A Likely benign same condition
- ACAA1 c.627-9T>C Likely benign same condition
- ACAA1 p.Asp75Glu Likely benign same condition
- ACAA1 p.Asp85= Likely benign same condition
- ACAA1 p.Gln2= Likely benign same condition
- ACAA1 p.Pro368= Likely benign same condition
- ACAA1 p.Glu172Asp Benign ★★ same type
- ACAA1 p.Ala131Ser 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/acaa1-p-ser154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown