CABP2 p.Leu20=
c.60C>T · rs950724245 · VCV1667462
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00253%, 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 -2.3 | GERP -3.3 |
| Overall | ||
| CADD | 1.651 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00253%
South Asian · 2/79,110 alleles
Filtering AF
0.00116%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000944%
Overall
0.00146%
22/1,509,114 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00253% | 39,555 |
| European (non-Finnish) | 0.00178% | 56,244 |
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.Leu20=
- Coding
- c.60C>T
- MANE Select
- NM_016366
- dbSNP
- rs950724245
- Type
- single nucleotide variant
- Location
- chr11:67522699 (GRCh38)
- Gene constraint
- LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.93
- Residue 20
- the 'disordered' region
Similar variants
- CABP2 p.Leu20Arg 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-leu20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown