CBY2
protein-codingchibby family member 2
Gene summary
Enables identical protein binding activity. Predicted to be located in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Jul 2025]
- SPERT
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CBY2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152719.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 82 | 2 | 84 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 83 | 2 | 0 | 85 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689932.1 | 3 | MANE Select | |
| Ensembl | ENSP00000309189.1 | 3 | MANE Select | |
| RefSeq | NP_001273270.1 | 2 | Standard | |
| RefSeq | NP_001273271.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of Wnt signaling pathway
- cilium assembly
- ciliary transition zone assembly
Molecular Function
- protein binding
Cellular Component
- centriole
- cytoplasmic vesicle
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000310521
- Coding exons
- 3
- Length
- 12249
- Individuals with no LoFs
- 114129
- Homozygous LoFs
- 408
- Heterozygous LoFs
- 11211
- Defined
- 125748
- p
- 0.0473
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.247 | 248 | 259 | 0.957 | 0.0000174 | 2878 |
| Missense (PolyPhen) | 98 | 99.183 | 0.98807 | 1124 | ||
| Synonymous | -0.395 | 126 | 120 | 1.05 | 0.00000856 | 892 |
| Loss of Function | 1.31 | 9 | 14.4 | 0.626 | 7.02e-7 | 172 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.13 | 0.12 | notable |
| Latino/Admixed American | 0.027 | 0.027 | notable |
| Ashkenazi Jewish | 0.060 | 0.059 | notable |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0.055 | 0.054 | notable |
| European (Non-Finnish) | 0.049 | 0.048 | notable |
| South Asian | 0.049 | 0.049 | notable |
| Other | 0.050 | 0.048 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.782
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |