COA6 p.Arg13=
c.39C>A · rs150519772 · VCV3024924
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.95%, 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 -1.9 | GERP -1.8 |
| Overall | ||
| CADD | 4.705 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.95%
East Asian · 423/44,542 alleles
Filtering AF
0.875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.846%
Overall
0.0349%
559/1,602,386 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.95% | 105 |
| Middle Eastern | 0.0663% | 1,508 |
| Remaining individualsnot grpmax-eligible | 0.0307% | 3,259 |
| Admixed American | 0.0224% | 4,456 |
| South Asian | 0.0211% | 4,747 |
| European (non-Finnish) | 0.00656% | 15,253 |
| Finnishnot grpmax-eligible | 0.00641% | 15,610 |
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.Arg13=
- Coding
- c.39C>A
- MANE Select
- NM_001206641
- dbSNP
- rs150519772
- Type
- single nucleotide variant
- Location
- chr1:234373505 (GRCh38)
- Gene constraint
- LOEUF 1.065 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.74 · 3 PDB
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-arg13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown