CABP4 p.Phe138=
c.414C>T · rs770861510 · VCV1561690
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00839%, nfe)
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 -3.7 | GERP -5 |
| Overall | ||
| CADD | 3.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00839%
European (non-Finnish) · 99/1,180,008 alleles
Filtering AF
0.00702%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00652%
Overall
0.00663%
107/1,613,864 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00839% | 11,919 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| South Asian | 0.00329% | 30,358 |
| African / African-American | 0.00267% | 37,512 |
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.Phe138=
- Coding
- c.414C>T
- MANE Select
- NM_145200
- dbSNP
- rs770861510
- Type
- single nucleotide variant
- Location
- chr11:67456315 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.01
- Residue 138
- the ef-hand 1 domain
Similar variants
- 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
- CABP4 p.Glu139Ter 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-phe138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown