CABP2 p.Arg92=
c.274C>A · rs761766884 · VCV2910594
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0286%, 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 0.07 | GERP -2, phastCons 0.001 |
| Overall | ||
| CADD | 7.941 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0286%
South Asian · 26/91,066 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0171%
Overall
0.00185%
27/1,461,104 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0286% | 3,503 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,494 |
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.Arg92=
- Coding
- c.274C>A
- MANE Select
- NM_016366
- dbSNP
- rs761766884
- Type
- single nucleotide variant
- Location
- chr11:67521130 (GRCh38)
- Gene constraint
- LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.93
- Residue 92
- the ef-hand 1 domain
Similar variants
- CABP2 p.Arg92Ter Pathogenic ★ same residue
- CABP2 p.Arg92Gln 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
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-arg92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown