CABP4 p.Pro64=
c.192C>G · rs1790765 · VCV1528779
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0157%, 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 -20 | GERP -4.3 |
| Overall | ||
| CADD | 0.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0157%
East Asian · 7/44,704 alleles
Filtering AF
0.00728%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00516%
Overall
0.000498%
8/1,607,296 alleles · ultra-rare
exomes 6/1,455,204 · genomes 2/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0157% | 6,386 |
| European (non-Finnish) | 8.49e-05% | 1,178,144 |
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.Pro64=
- Coding
- c.192C>G
- MANE Select
- NM_145200
- dbSNP
- rs1790765
- Type
- single nucleotide variant
- Location
- chr11:67455615 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.01
- Residue 64
- the 'disordered' region
Similar variants
- GPR152 p.Thr64Met 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-pro64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown