CABP2 p.Pro41=
c.123C>T · VCV3714927
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00716%, 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 -3.6 | GERP -2.6 |
| Overall | ||
| CADD | 0.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00716%
South Asian · 6/83,828 alleles
Filtering AF
0.00307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00209%
Overall
0.00103%
16/1,547,556 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00716% | 13,971 |
| Admixed American | 0.00591% | 16,929 |
| African / African-American | 0.00274% | 36,481 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,922 |
| European (non-Finnish) | 0.000349% | 286,366 |
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
- CABP2
- Protein
- p.Pro41=
- Coding
- c.123C>T
- MANE Select
- NM_016366
- Type
- single nucleotide variant
- Location
- chr11:67522636 (GRCh38)
- Gene constraint
- LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.93
- Residue 41
- the 'disordered' region
Similar variants
- CABP2 c.637+1G>T Pathogenic/Likely pathogenic ★★ same type
- CABP2 p.Ala183Thr Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg101Gln Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg108Gln Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg11Gln Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg216Gln Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg220Gln Uncertain significance ★★ ⚠ same type
- CABP2 p.Arg73Gln 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/cabp2-p-pro41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown