COA7 p.Val13=
c.39C>T · VCV4085923
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.72 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 10.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,008 alleles
Overall
0.000124%
2/1,612,734 alleles · very rare
exomes 2/1,460,408 · genomes 0/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,008 |
| South Asian | 0.0011% | 91,070 |
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
- COA7
- Protein
- p.Val13=
- Coding
- c.39C>T
- MANE Select
- NM_023077
- Type
- single nucleotide variant
- Location
- chr1:52698288 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 95.47 · 1 PDB
- Residue 13
- an α-helix
Similar variants
- COA7 p.Glu220Gln Uncertain significance ★★ ⚠ same type
- COA7 p.Glu31Lys Uncertain significance ★★ ⚠ same type
- COA7 p.Gly84Asp Uncertain significance ★★ ⚠ same type
- COA7 p.Tyr38Cys Uncertain significance ★★ ⚠ same type
- COA7 c.107-20C>G Benign/Likely benign ★★ same type
- COA7 c.107-5C>T Likely benign ★★ same type
- COA7 c.248-145C>T Benign ★★ same type
- COA7 c.248-36C>G Benign ★★ 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/coa7-p-val13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown