CABP4 p.Pro88=
c.264T>C · rs1402092785 · VCV1574210
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00336%, amr)
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 -3.8 | GERP -4.1 |
| Overall | ||
| CADD | 0.809 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00336%
Admixed American · 2/59,524 alleles
Filtering AF
0.000557%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000209%
Overall
0.000124%
2/1,607,222 alleles · very rare
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
- CABP4
- Protein
- p.Pro88=
- Coding
- c.264T>C
- MANE Select
- NM_145200
- dbSNP
- rs1402092785
- Type
- single nucleotide variant
- Location
- chr11:67455687 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.01
- Residue 88
- the 'disordered' region
Similar variants
- CABP4 p.Pro88Ser Uncertain significance ★ ⚠ same residue
- CABP4 c.366+1G>T Pathogenic/Likely pathogenic ★★ same type
- CABP4 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same type
- CABP4 p.Arg216Ter Pathogenic ★★ same type
- CABP4 p.Arg225Ter Pathogenic ★★ same type
- CABP4 p.Arg49Ter Pathogenic/Likely pathogenic ★★ same type
- CABP4 p.Arg52Ter Pathogenic ★★ same type
- CABP4 p.Arg98Ter Pathogenic/Likely pathogenic ★★ 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/cabp4-p-pro88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown