CPOX p.Leu15=
c.45C>T · VCV4690557
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, 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 0.06 | GERP -0.98 |
| Overall | ||
| CADD | 6.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
South Asian · 12/79,802 alleles
Filtering AF
0.00859%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00671%
Overall
0.00201%
30/1,493,764 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.015% | 6,650 |
| African / African-American | 0.00867% | 11,529 |
| East Asian | 0.00834% | 11,993 |
| Admixed American | 0.00653% | 15,306 |
| European (non-Finnish) | 0.000532% | 188,065 |
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
- CPOX
- Protein
- p.Leu15=
- Coding
- c.45C>T
- MANE Select
- NM_000097
- Type
- single nucleotide variant
- Location
- chr3:98593460 (GRCh38)
- Gene constraint
- LOEUF 0.8 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.32 · 1 PDB
Similar variants
- CPOX p.Cys239Ter Pathogenic ★★ same type
- CPOX p.Gln160Ter Pathogenic ★★ same type
- CPOX p.Glu201Lys Pathogenic/Likely pathogenic ★★ same type
- CPOX p.Lys404Glu Pathogenic/Likely pathogenic ★★ same type
- CPOX c.811+5G>C Uncertain significance ★★ same type
- CPOX p.Ala293Thr Uncertain significance ★★ ⚠ same type
- CPOX p.Ala83Val Uncertain significance ★★ ⚠ same type
- CPOX p.Ala89Val 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/cpox-p-leu15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown