COQ9 p.Ala5=
c.15G>A · VCV4705411
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00306%, eas)
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 -1.2 | GERP -3.5 |
| Overall | ||
| CADD | 8.101 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00306%
East Asian · 1/32,646 alleles
Filtering AF
0.000625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000494%
Overall
0.00122%
16/1,310,264 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00306% | 32,646 |
| South Asian | 0.00247% | 40,508 |
| Finnishnot grpmax-eligible | 0.00219% | 45,618 |
| African / African-American | 0.00153% | 65,466 |
| European (non-Finnish) | 0.00117% | 85,297 |
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.Ala5=
- Coding
- c.15G>A
- MANE Select
- NM_020312
- Type
- single nucleotide variant
- Location
- chr16:57447520 (GRCh38)
- Gene constraint
- LOEUF 1.035 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.16 · 5 PDB
Similar variants
- COQ9 p.Ala5Gly Uncertain significance ★★ ⚠ same residue
- COQ9 p.Ala5Val Uncertain significance ★★ ⚠ same residue
- COQ9 p.Ala5Glu Uncertain significance ★ ⚠ same residue
- COQ9 p.Ala5dup Uncertain significance ★ 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
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-ala5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown