CABP4 p.Leu14=
c.42G>C · rs1216850071 · VCV1084483
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, 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 -4.2 | GERP -3.1 |
| Overall | ||
| CADD | 0.217 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,842 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00296%
Overall
0.000411%
6/1,459,252 alleles · ultra-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.Leu14=
- Coding
- c.42G>C
- MANE Select
- NM_145200
- dbSNP
- rs1216850071
- Type
- single nucleotide variant
- Location
- chr11:67455465 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.01
- Residue 14
- the 'disordered' region
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-leu14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown