COQ2 p.Pro73=
c.219G>T · rs549493176 · VCV1900531
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0522%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -2.9, phastCons 0.99 |
| Overall | ||
| CADD | 11.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0522%
East Asian · 22/42,118 alleles
Filtering AF
0.0353%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0298%
Overall
0.00165%
26/1,573,966 alleles · ultra-rare
exomes 18/1,421,628 · genomes 8/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0522% | 1,914 |
| South Asian | 0.00348% | 28,714 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,902 |
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
- COQ2
- Protein
- p.Pro73=
- Coding
- c.219G>T
- MANE Select
- NM_001358921
- dbSNP
- rs549493176
- Type
- single nucleotide variant
- Location
- chr4:83284546 (GRCh38)
- Gene constraint
- LOEUF 1.032 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.64
Similar variants
- COQ2 p.Arg123Cys Likely pathogenic ★★ same type
- COQ2 p.Arg147His Pathogenic/Likely pathogenic ★★ same type
- COQ2 p.Gln44Ter Likely pathogenic ★★ same type
- COQ2 p.Ser96Asn Pathogenic ★★ same type
- COQ2 p.Trp24Ter Likely pathogenic ★★ same type
- COQ2 p.Trp87Ter Pathogenic/Likely pathogenic ★★ same type
- COQ2 c.-26G>C Uncertain significance ★★ same type
- COQ2 c.-4C>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/coq2-p-pro73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown