COQ9 p.Ala9=
c.27G>A · rs1201340269 · VCV1963668
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00763%, afr)
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 -1.7 | GERP -4.1 |
| Overall | ||
| CADD | 2.984 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00763%
African / African-American · 5/65,516 alleles
Filtering AF
0.00293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00192%
Overall
0.000951%
11/1,156,520 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00763% | 13,103 |
| Remaining individualsnot grpmax-eligible | 0.00622% | 16,087 |
| Admixed American | 0.00347% | 28,816 |
| South Asian | 0.00249% | 40,194 |
| European (non-Finnish) | 9.77e-05% | 1,023,230 |
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
- COQ9
- Protein
- p.Ala9=
- Coding
- c.27G>A
- MANE Select
- NM_020312
- dbSNP
- rs1201340269
- Type
- single nucleotide variant
- Location
- chr16:57447532 (GRCh38)
- Gene constraint
- LOEUF 1.035 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.16 · 5 PDB
Similar variants
- COQ9 p.Ala9Pro Uncertain significance ★★ ⚠ same residue
- COQ9 p.Ala9Ser Uncertain significance ★★ ⚠ same residue
- COQ9 p.Ala9Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- COQ9 c.522-1G>A Likely pathogenic ★★ same type
- COQ9 c.711+3G>C Pathogenic ★★ same type
- COQ9 p.Arg244Ter Pathogenic/Likely pathogenic ★★ same type
- COQ9 p.Arg29Ter Pathogenic/Likely pathogenic ★★ same type
- COQ9 c.242+5G>A 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/coq9-p-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown