COQ2 p.Pro83=
c.249C>T · rs748175494 · VCV2135132
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00182%, amr)
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 0.39 | GERP -1.5, phastCons 0.99 |
| Overall | ||
| CADD | 13.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00182%
Admixed American · 1/54,910 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000254%
4/1,572,652 alleles · very rare
exomes 2/1,420,458 · genomes 2/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00182% | 54,910 |
| African / African-American | 0.00137% | 72,738 |
| European (non-Finnish) | 0.000172% | 580,636 |
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.Pro83=
- Coding
- c.249C>T
- MANE Select
- NM_001358921
- dbSNP
- rs748175494
- Type
- single nucleotide variant
- Location
- chr4:83284516 (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-pro83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown