ACAA1 p.Gln2=
c.6G>A · rs759096151 · VCV3042154
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0038%, nfe)
Conditions
1
ACAA1-related disorder
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 0.28 | GERP -3, phastCons 0.022 |
| Overall | ||
| CADD | 8.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0038%
European (non-Finnish) · 44/1,157,300 alleles
Filtering AF
0.00288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00257%
Overall
0.00294%
46/1,564,148 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0038% | 26,302 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,308 |
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.Gln2=
- Coding
- c.6G>A
- MANE Select
- NM_001607
- dbSNP
- rs759096151
- Type
- single nucleotide variant
- Location
- chr3:38137030 (GRCh38)
- Gene constraint
- LOEUF 1.199 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.93 · 2 PDB
- Residue 2
- the 'pts2-type peroxisomal targeting signal' region
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.Pro368= Likely benign same condition
- ACAA1 p.Ser154= 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-gln2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown