CCBE1 p.Gln84=
c.252A>G · rs201929225 · VCV2794135
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, 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 -5.5 | GERP -4.8 |
| Overall | ||
| CADD | 1.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,538 alleles
Overall
0.000125%
2/1,595,568 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,538 |
| European (non-Finnish) | 8.59e-05% | 1,163,701 |
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.Gln84=
- Coding
- c.252A>G
- MANE Select
- NM_133459
- dbSNP
- rs201929225
- Type
- single nucleotide variant
- Location
- chr18:59480199 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.61
Similar variants
- 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
- CCBE1 p.Ala96Gly 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-gln84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown