CABP2 p.Ala149=
c.447A>G · rs137889404 · VCV2995489
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00873%, 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 -8.9 | GERP -3.9 |
| Overall | ||
| CADD | 3.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00873%
European (non-Finnish) · 103/1,180,012 alleles
Filtering AF
0.00733%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00684%
Overall
0.00644%
104/1,613,786 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00873% | 11,456 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
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.Ala149=
- Coding
- c.447A>G
- MANE Select
- NM_016366
- dbSNP
- rs137889404
- Type
- single nucleotide variant
- Location
- chr11:67520093 (GRCh38)
- Gene constraint
- LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.93
Similar variants
- CABP2 p.Ala149Glu Uncertain significance ★ same residue
- 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
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-ala149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown