CCBE1 p.Cys159=
c.477C>T · rs149268172 · VCV1568959
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0507%, afr)
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 -0.33 | GERP -4.7, phastCons 0.001 |
| Overall | ||
| CADD | 5.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0507%
African / African-American · 38/75,022 alleles
Filtering AF
0.0379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0334%
Overall
0.00471%
76/1,613,622 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0507% | 1,974 |
| South Asian | 0.0176% | 5,691 |
| Middle Eastern | 0.0171% | 5,844 |
| East Asian | 0.00891% | 11,218 |
| Admixed American | 0.00333% | 30,008 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| Finnishnot grpmax-eligible | 0.00156% | 63,970 |
| European (non-Finnish) | 0.0011% | 90,757 |
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
- CCBE1
- Protein
- p.Cys159=
- Coding
- c.477C>T
- MANE Select
- NM_133459
- dbSNP
- rs149268172
- Type
- single nucleotide variant
- Location
- chr18:59466815 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.61
- Residue 159
- a disulfide bond; the egf-like; calcium-binding domain
Similar variants
- CCBE1 p.Cys159Ter Pathogenic ★ same residue
- CCBE1 p.Arg108Ter Pathogenic ★★ same type
- CCBE1 p.Arg118Ter Pathogenic/Likely pathogenic ★★ same type
- CCBE1 c.654+5G>C Uncertain significance ★★ same type
- CCBE1 c.*203A>G Uncertain significance ★★ same type
- CCBE1 c.*4173A>G Uncertain significance ★★ same type
- CCBE1 p.Ala28Val Uncertain significance ★★ ⚠ same type
- CCBE1 p.Ala322Val Uncertain significance ★★ ⚠ 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/ccbe1-p-cys159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown