CABP2 p.Tyr112=
c.336C>T · VCV3707157
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0314%, eas)
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 2.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 7.723 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0314%
East Asian · 14/44,644 alleles
Filtering AF
0.0189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.00212%
34/1,606,492 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0314% | 3,189 |
| African / African-American | 0.0151% | 6,633 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,784 |
| South Asian | 0.0011% | 90,582 |
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.Tyr112=
- Coding
- c.336C>T
- MANE Select
- NM_016366
- Type
- single nucleotide variant
- Location
- chr11:67521068 (GRCh38)
- Gene constraint
- LOEUF 1.299 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.93
- Residue 112
- the ef-hand 1 domain
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-tyr112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown