COX16 p.Ser65=
c.195G>A · rs372378281 · VCV3076444
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0943%, amr)
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 -0.03 | GERP -2.5, phastCons 0.93 |
| Overall | ||
| CADD | 11.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0943%
Admixed American · 55/58,322 alleles
Filtering AF
0.0744%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0672%
Overall
0.00661%
105/1,588,980 alleles · ultra-rare
exomes 56/1,437,934 · genomes 49/151,046 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0943% | 1,060 |
| African / African-American | 0.0122% | 8,207 |
| Remaining individualsnot grpmax-eligible | 0.00984% | 10,165 |
| European (non-Finnish) | 0.00283% | 35,293 |
| Finnishnot grpmax-eligible | 0.00159% | 62,770 |
| South Asian | 0.00112% | 89,620 |
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
- COX16
- Protein
- p.Ser65=
- Coding
- c.195G>A
- MANE Select
- NM_016468
- dbSNP
- rs372378281
- Type
- single nucleotide variant
- Location
- chr14:70329183 (GRCh38)
- Gene constraint
- LOEUF 1.373 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.50
Similar variants
- COX16 p.Ser65Leu Uncertain significance ★ ⚠ same residue
- COX16 p.Ser62Pro Uncertain significance ★★ ⚠ same type
- COX16 c.141+10A>G Uncertain significance ★ same type
- COX16 p.Arg11Leu Uncertain significance ★ ⚠ same type
- COX16 p.Arg34His Uncertain significance ★ ⚠ same type
- COX16 p.Asn80Asp Uncertain significance ★ ⚠ same type
- COX16 p.Gly17Ser Uncertain significance ★ ⚠ same type
- COX16 p.Ile70Met 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/cox16-p-ser65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown