COX5B p.Arg7=
c.21C>T · rs114574573 · VCV2651169
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, nfe)
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 -1.8 | GERP -1.5 |
| Overall | ||
| CADD | 11.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
European (non-Finnish) · 11,853/1,149,702 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.82%
12,763/1,556,448 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.03% | 97 |
| Remaining individualsnot grpmax-eligible | 0.889% | 112 |
| Middle Eastern | 0.567% | 176 |
| Admixed American | 0.228% | 439 |
| African / African-American | 0.176% | 570 |
| Ashkenazi Jewishnot grpmax-eligible | 0.126% | 797 |
| Finnishnot grpmax-eligible | 0.0518% | 1,931 |
| South Asian | 0.0308% | 3,247 |
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
- COX5B
- Protein
- p.Arg7=
- Coding
- c.21C>T
- MANE Select
- NM_001862
- dbSNP
- rs114574573
- Type
- single nucleotide variant
- Location
- chr2:97646107 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 85.75 · 3 PDB
Similar variants
- COX5B p.Arg7Cys Uncertain significance ★ ⚠ same residue
- COX5B c.278-1G>A Uncertain significance ★ same type
- COX5B p.Ala54Val Uncertain significance ★ ⚠ same type
- COX5B p.Arg112Gln Uncertain significance ★ ⚠ same type
- COX5B p.Arg29Cys Uncertain significance ★ ⚠ same type
- COX5B p.Arg4Ser Uncertain significance ★ ⚠ same type
- COX5B p.Glu109Lys Uncertain significance ★ ⚠ same type
- COX5B p.Gly10Ala 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/cox5b-p-arg7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown