CTNND1
Basic information
Region (hg38): 11:57753243-57819546
Previous symbols: [ "CTNND" ]
Links
Phenotypes
GenCC
Source:
- blepharocheilodontic syndrome 2 (Definitive), mode of inheritance: AD
- blepharocheilodontic syndrome (Supportive), mode of inheritance: AD
- blepharocheilodontic syndrome 2 (Strong), mode of inheritance: AD
- blepharocheilodontic syndrome 2 (Strong), mode of inheritance: AD
- blepharocheilodontic syndrome 2 (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Blepharocheilodontic syndrome 2 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dermatologic; Dental | 28301459 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (110 variants)
- not_provided (83 variants)
- CTNND1-related_disorder (23 variants)
- Blepharocheilodontic_syndrome_2 (22 variants)
- Cleft_lip_with_or_without_cleft_palate (11 variants)
- not_specified (5 variants)
- Leber_congenital_amaurosis_2 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNND1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001085458.2. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 10 | 13 | ||||
missense | 158 | 13 | 179 | |||
nonsense | 15 | |||||
start loss | 0 | |||||
frameshift | 9 | |||||
splice donor/acceptor (+/-2bp) | 6 | |||||
Total | 17 | 14 | 162 | 23 | 6 |
Highest pathogenic variant AF is 0.00000136843
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CTNND1 | protein_coding | protein_coding | ENST00000399050 | 19 | 66304 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.0000115 | 124648 | 0 | 8 | 124656 | 0.0000321 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.08 | 432 | 572 | 0.756 | 0.0000352 | 6260 |
Missense in Polyphen | 141 | 215.27 | 0.65498 | 2269 | ||
Synonymous | 2.19 | 160 | 199 | 0.803 | 0.0000105 | 1913 |
Loss of Function | 6.00 | 4 | 49.6 | 0.0806 | 0.00000277 | 588 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000566 | 0.0000556 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000451 | 0.0000442 |
Middle Eastern | 0.0000566 | 0.0000556 |
South Asian | 0.0000354 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to and inhibits the transcriptional repressor ZBTB33, which may lead to activation of target genes of the Wnt signaling pathway (By similarity). Associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability. Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors. Promotes GLIS2 C-terminal cleavage. {ECO:0000250, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.;
- Disease
- DISEASE: Blepharocheilodontic syndrome 2 (BCDS2) [MIM:617681]: A form of blepharocheilodontic syndrome, a rare autosomal dominant disorder. It is characterized by lower eyelid ectropion, upper eyelid distichiasis, euryblepharon, bilateral cleft lip and palate, and features of ectodermal dysplasia, including hair anomalies, conical teeth and tooth agenesis. An additional rare manifestation is imperforate anus. There is considerable phenotypic variability among affected individuals. {ECO:0000269|PubMed:28301459}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Adherens junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Wnt Signaling Pathway and Pluripotency;Disease;Signal Transduction;VEGFA-VEGFR2 Pathway;Infectious disease;EGFR1;E-cadherin signaling in keratinocytes;Posttranslational regulation of adherens junction stability and dissassembly;Signaling by VEGF;Arf6 trafficking events;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Signaling by Receptor Tyrosine Kinases;Cell-Cell communication;Stabilization and expansion of the E-cadherin adherens junction;N-cadherin signaling events;FGF signaling pathway;E-cadherin signaling in the nascent adherens junction;VEGFR2 mediated vascular permeability;InlA-mediated entry of Listeria monocytogenes into host cells;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.272
Intolerance Scores
- loftool
- 0.538
- rvis_EVS
- -0.73
- rvis_percentile_EVS
- 14.2
Haploinsufficiency Scores
- pHI
- 0.749
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.590
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.664
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctnnd1
- Phenotype
- cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; renal/urinary system 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); vision/eye phenotype; 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); neoplasm;
Zebrafish Information Network
- Gene name
- ctnnd1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- cell-cell junction assembly;cell adhesion;brain development;Wnt signaling pathway;adherens junction organization;entry of bacterium into host cell;negative regulation of canonical Wnt signaling pathway;cell-cell adhesion;regulation of postsynaptic membrane neurotransmitter receptor levels
- Cellular component
- nucleus;cytoplasm;cytosol;plasma membrane;cell-cell junction;cell-cell adherens junction;zonula adherens;catenin complex;lamellipodium;growth cone;midbody;dendritic spine;extracellular exosome;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;presynaptic active zone cytoplasmic component;glutamatergic synapse;postsynaptic density, intracellular component
- Molecular function
- signaling receptor binding;protein binding;protein kinase binding;cadherin binding