COX10 p.Thr172=
c.516C>T · rs758296972 · VCV2994321
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 2.4 | GERP 0.75, phastCons 1 |
| Overall | ||
| CADD | 9.813 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,082 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000342%
5/1,461,430 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,082 |
| European (non-Finnish) | 0.000339% | 294,929 |
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
- COX10
- Protein
- p.Thr172=
- Coding
- c.516C>T
- MANE Select
- NM_001303
- dbSNP
- rs758296972
- Type
- single nucleotide variant
- Location
- chr17:14102134 (GRCh38)
- Gene constraint
- LOEUF 0.934 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.11
Similar variants
- COX10 p.Thr172Ala Uncertain significance ★ ⚠ same residue
- COX10 p.Asp336Val Pathogenic/Likely pathogenic ★★ same type
- COX10 p.Gln230Ter Likely pathogenic ★★ same type
- COX10 p.Pro225Leu Likely pathogenic ★★ same type
- COX10 c.-89G>C Uncertain significance ★★ same type
- COX10 c.-89G>T Uncertain significance ★★ same type
- COX10 p.Ala174Thr Uncertain significance ★★ ⚠ same type
- COX10 p.Ala175Ser 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/cox10-p-thr172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown