COX6A1 p.Thr92=
c.276T>C · rs2137032189 · VCV1538756
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.33 | GERP -3.7, phastCons 0.27 |
| Overall | ||
| CADD | 6.212 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- COX6A1
- Protein
- p.Thr92=
- Coding
- c.276T>C
- MANE Select
- NM_004373
- dbSNP
- rs2137032189
- Type
- single nucleotide variant
- Location
- chr12:120440483 (GRCh38)
- Gene constraint
- LOEUF 1.355 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 84.06 · 3 PDB
Similar variants
- COX6A1 c.103+1G>C Uncertain significance ★★ same type
- COX6A1 p.Ala2Ser Uncertain significance ★★ ⚠ same type
- COX6A1 p.Arg11Pro Uncertain significance ★★ ⚠ same type
- COX6A1 p.Arg17His Uncertain significance ★★ ⚠ same type
- COX6A1 p.Arg36Cys Uncertain significance ★★ ⚠ same type
- COX6A1 p.Glu107Lys Uncertain significance ★★ ⚠ same type
- COX6A1 p.His62Tyr Uncertain significance ★★ ⚠ same type
- COX6A1 p.His98Tyr 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/cox6a1-p-thr92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown