ACACA p.Ser789=
c.2367G>A · rs367784761 · VCV3052495
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.09%, sas)
Conditions
1
ACACA-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 -10 | GERP -4 |
| Overall | ||
| CADD | 1.774 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.09%
South Asian · 82/91,064 alleles
Filtering AF
0.0743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0685%
Overall
0.00576%
93/1,613,942 alleles · ultra-rare
exomes 90/1,461,868 · genomes 3/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.09% | 1,111 |
| Middle Eastern | 0.0164% | 6,084 |
| East Asian | 0.00668% | 14,963 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| African / African-American | 0.00267% | 37,449 |
| European (non-Finnish) | 0.000254% | 393,331 |
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
- ACACA
- Protein
- p.Ser789=
- Coding
- c.2367G>A
- MANE Select
- NM_198834
- dbSNP
- rs367784761
- Type
- single nucleotide variant
- Location
- chr17:37246919 (GRCh38)
- Gene constraint
- LOEUF 0.374 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05 · 10 PDB
- Residue 789
- a β-strand; the biotinyl-binding domain
Disease context
ACACA-related disorder
Similar variants
- ACACA c.5569-10C>G Likely benign same condition
- ACACA p.Asn990= Likely benign same condition
- ACACA p.Leu1734= Likely benign same condition
- ACACA p.Val2008= Likely benign same condition
- ACACA p.Pro699fs Uncertain significance same condition
- ACACA c.4777-8del Likely benign same condition
- ACACA p.Ala2308Val Uncertain significance ★★ ⚠ same type
- ACACA p.Arg1206His 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/acaca-p-ser789 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown