Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 6.96%, sas) — too common for a highly-penetrant pathogenic allele
Conditions
1
acyl-CoA dehydrogenase 9 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 -0.42 | GERP -2.8, phastCons 0.063 |
| Overall | ||
| CADD | 6.277 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.96%
South Asian · 6,341/91,084 alleles
Filtering AF
6.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.76%
Overall
1.77%
28,518/1,614,078 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 6.96% | 14 |
| African / African-American | 5.24% | 19 |
| East Asian | 5.14% | 19 |
| Finnishnot grpmax-eligible | 4.05% | 25 |
| Remaining individualsnot grpmax-eligible | 2.18% | 46 |
| Ashkenazi Jewishnot grpmax-eligible | 1.93% | 52 |
| Admixed American | 1.03% | 97 |
| European (non-Finnish) | 0.91% | 110 |
| Middle Eastern | 0.808% | 124 |
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
- ACAD9
- Protein
- p.Leu263=
- Coding
- c.787T>C
- MANE Select
- NM_014049
- dbSNP
- rs1979529
- Type
- single nucleotide variant
- Location
- chr3:128899440 (GRCh38)
- Gene constraint
- LOEUF 0.884 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.09 · 2 PDB
- Residue 263
- a β-strand
Disease context
acyl-CoA dehydrogenase 9 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Acyl-CoA dehydrogenase 9 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- ACAD9 c.1150-2A>G Likely pathogenic ★★ same condition
- ACAD9 c.1278+1G>T Likely pathogenic ★★ same condition
- ACAD9 c.1279-2A>C Likely pathogenic ★★ same condition
- ACAD9 c.1358+2T>G Likely pathogenic ★★ same condition
- ACAD9 c.1359-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACAD9 c.1563+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACAD9 c.1A>G Pathogenic/Likely pathogenic ★★ same condition
- ACAD9 c.453+1G>A Likely 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/acad9-p-leu263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown