CCBE1 p.Ser63=
c.189A>G · rs141422782 · VCV1563115
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, sas)
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 -5.5 |
| Overall | ||
| CADD | 5.839 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
South Asian · 19/91,092 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00428%
69/1,613,962 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,794 |
| Middle Eastern | 0.0165% | 6,070 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,824 |
| European (non-Finnish) | 0.00373% | 26,817 |
| African / African-American | 0.00267% | 37,472 |
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.Ser63=
- Coding
- c.189A>G
- MANE Select
- NM_133459
- dbSNP
- rs141422782
- Type
- single nucleotide variant
- Location
- chr18:59696652 (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-ser63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown