COA6 p.Val15=
c.45G>A · rs752001515 · VCV3058720
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, amr)
Conditions
1
COA6-related disorder
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>C here scores Δ0.77 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.27 | gain · loss 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -1.1, phastCons 0.016 |
| Overall | ||
| CADD | 7.513 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
Admixed American · 11/58,908 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00809%
Overall
0.000825%
12/1,454,780 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0187% | 5,355 |
| European (non-Finnish) | 8.5e-05% | 1,176,822 |
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
- COA6
- Protein
- p.Val15=
- Coding
- c.45G>A
- MANE Select
- NM_001206641
- dbSNP
- rs752001515
- Type
- single nucleotide variant
- Location
- chr1:234373511 (GRCh38)
- Gene constraint
- LOEUF 1.065 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.74 · 3 PDB
Disease context
COA6-related disorder
Similar variants
- COA6 c.212+114G>T Uncertain significance ★★ ⚠ same type
- COA6 p.Met82Val Uncertain significance ★★ ⚠ same type
- COA6 p.Ser114Gly Uncertain significance ★★ ⚠ same type
- COA6 c.212+144C>G Benign/Likely benign ★★ same type
- COA6 c.212+154A>G Likely benign ★★ same type
- COA6 c.212+162G>A Benign/Likely benign ★★ ⚠ same type
- COA6 c.213-105T>G Likely benign ★★ same type
- COA6 c.213-111T>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/coa6-p-val15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown