CPXM2 p.Ala172=
c.516G>A · rs138633933 · VCV787082
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.07%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.57 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -5.1 |
| Overall | ||
| CADD | 15.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.07%
African / African-American · 1,551/74,986 alleles
Filtering AF
1.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.95%
Overall
0.106%
1,712/1,613,898 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.07% | 48 |
| Remaining individualsnot grpmax-eligible | 0.112% | 893 |
| Admixed American | 0.0867% | 1,154 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00297% | 33,711 |
| South Asian | 0.0022% | 45,532 |
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
- CPXM2
- Protein
- p.Ala172=
- Coding
- c.516G>A
- MANE Select
- NM_198148
- dbSNP
- rs138633933
- Type
- single nucleotide variant
- Location
- chr10:123842486 (GRCh38)
- Gene constraint
- LOEUF 0.974 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.58
- Residue 172
- a disulfide bond; the f5/8 type c domain
Similar variants
- CPXM2 c.1918-10T>C Benign ★★ same type
- CPXM2 p.Lys577Arg Benign ★★ same type
- CPXM2 p.Ala153Asp Uncertain significance ★ ⚠ same type
- CPXM2 p.Ala183Val Uncertain significance ★ ⚠ same type
- CPXM2 p.Ala376Val Uncertain significance ★ ⚠ same type
- CPXM2 p.Ala402Val Uncertain significance ★ ⚠ same type
- CPXM2 p.Ala524Ser Uncertain significance ★ ⚠ same type
- CPXM2 p.Ala565Asp 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/cpxm2-p-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown