CABP4 p.Ala23=
c.69G>A · rs775292545 · VCV305640
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0271%, amr)
Conditions
2
Inborn genetic diseases
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 -1.2 | GERP -3.6 |
| Overall | ||
| CADD | 3.379 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0271%
Admixed American · 16/58,984 alleles
Filtering AF
0.017%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.00448%
72/1,607,960 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0271% | 3,687 |
| Middle Eastern | 0.0166% | 6,012 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,919 |
| European (non-Finnish) | 0.00365% | 27,398 |
| South Asian | 0.00222% | 45,026 |
| African / African-American | 0.00133% | 75,044 |
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.Ala23=
- Coding
- c.69G>A
- MANE Select
- NM_145200
- dbSNP
- rs775292545
- Type
- single nucleotide variant
- Location
- chr11:67455492 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.01
- Residue 23
- the 'disordered' region
Similar variants
- CABP4 p.Ala23Val Likely benign ★★ same residue
- CABP4 p.Ala23Gly Uncertain significance ★ ⚠ same residue
- CABP4 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same condition
- CABP4 p.Arg216Ter Pathogenic ★★ same condition
- CABP4 p.Arg225Ter Pathogenic ★★ same condition
- CABP4 p.Arg49Ter Pathogenic/Likely pathogenic ★★ same condition
- CABP4 p.Arg52Ter Pathogenic ★★ same condition
- CABP4 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same condition
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-ala23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown