COA6 p.Ser24=
c.72T>C · rs759571894 · VCV514919
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.105%, 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 0.011 | GERP -0.32 |
| Overall | ||
| CADD | 6.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
East Asian · 47/44,850 alleles
Filtering AF
0.0809%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0725%
Overall
0.00801%
129/1,610,668 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.105% | 954 |
| South Asian | 0.0737% | 1,357 |
| Remaining individualsnot grpmax-eligible | 0.0241% | 4,150 |
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.Ser24=
- Coding
- c.72T>C
- MANE Select
- NM_001206641
- dbSNP
- rs759571894
- Type
- single nucleotide variant
- Location
- chr1:234373538 (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-ser24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown