CTNNBIP1
catenin beta interacting protein 1
Basic information
Region (hg38): 1:9848276-9910336
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNNBIP1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in CTNNBIP1
This is a list of pathogenic ClinVar variants found in the CTNNBIP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-9871204-G-A | not specified | Uncertain significance (May 23, 2024) | ||
| 1-9871229-T-C | not specified | Uncertain significance (May 26, 2022) | ||
| 1-9871231-A-C | not specified | Uncertain significance (Aug 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTNNBIP1 | protein_coding | protein_coding | ENST00000377263 | 3 | 62061 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0248 | 0.793 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.529 | 43 | 53.9 | 0.797 | 0.00000370 | 516 |
| Missense in Polyphen | 17 | 16.794 | 1.0123 | 170 | ||
| Synonymous | -1.06 | 27 | 20.8 | 1.30 | 0.00000153 | 150 |
| Loss of Function | 0.991 | 3 | 5.51 | 0.544 | 4.19e-7 | 47 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Prevents the interaction between CTNNB1 and TCF family members, and acts as negative regulator of the Wnt signaling pathway. {ECO:0000269|PubMed:12408824}.;
- Pathway
- Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;Wnt Canonical;Regulation of nuclear beta catenin signaling and target gene transcription;TCF dependent signaling in response to WNT;Wnt Mammals
(Consensus)
Intolerance Scores
- loftool
- 0.459
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.95
Haploinsufficiency Scores
- pHI
- 0.219
- hipred
- Y
- hipred_score
- 0.719
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.448
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctnnbip1
- Phenotype
- growth/size/body region phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; embryo phenotype; renal/urinary system phenotype; skeleton phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- branching involved in ureteric bud morphogenesis;regulation of vascular permeability involved in acute inflammatory response;anterior/posterior pattern specification;Wnt signaling pathway;negative regulation of Wnt signaling pathway;negative regulation of protein binding;negative regulation of DNA binding;negative regulation of DNA-binding transcription factor activity;positive regulation of monocyte differentiation;positive regulation of osteoblast differentiation;negative regulation of smooth muscle cell proliferation;negative regulation of transcription initiation from RNA polymerase II promoter;negative regulation of mesenchymal cell proliferation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;beta-catenin destruction complex
- Molecular function
- protein binding;beta-catenin binding;armadillo repeat domain binding