CTNNA2
catenin alpha 2, the group of Alpha catenins
Basic information
Region (hg38): 2:79185231-80648861
Links
Phenotypes
GenCC
Source:
- cortical dysplasia, complex, with other brain malformations 9 (Moderate), mode of inheritance: AR
- cortical dysplasia, complex, with other brain malformations 9 (Strong), mode of inheritance: AR
- cortical dysplasia, complex, with other brain malformations 9 (Strong), mode of inheritance: AR
- cortical dysplasia, complex, with other brain malformations 9 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cortical dysplasia, complex, with other brain malformations, 9 | AR | 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 | Neurologic | 30013181 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (53 variants)
- not_provided (50 variants)
- not_specified (49 variants)
- CTNNA2-related_disorder (21 variants)
- Cortical_dysplasia,_complex,_with_other_brain_malformations_9 (10 variants)
- Hereditary_breast_ovarian_cancer_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNNA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001282597.3. 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 | 20 | 25 | ||||
| missense | 68 | 70 | ||||
| nonsense | 5 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 5 | 3 | 70 | 21 | 5 |
Highest pathogenic variant AF is 0.0000065731524
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTNNA2 | protein_coding | protein_coding | ENST00000466387 | 17 | 1463549 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.425 | 0.575 | 125264 | 0 | 21 | 125285 | 0.0000838 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.63 | 306 | 544 | 0.562 | 0.0000329 | 5931 |
| Missense in Polyphen | 72 | 158.38 | 0.45461 | 1732 | ||
| Synonymous | -0.223 | 221 | 217 | 1.02 | 0.0000144 | 1775 |
| Loss of Function | 4.82 | 10 | 44.8 | 0.223 | 0.00000263 | 496 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000159 | 0.000157 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000621 | 0.0000617 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000294 | 0.000294 |
| Other | 0.000167 | 0.000164 |
dbNSFP
Source:
- Function
- FUNCTION: May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation. {ECO:0000250|UniProtKB:Q61301}.;
- Pathway
- Gastric cancer - Homo sapiens (human);Adherens junction - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy;Ectoderm Differentiation;Endometrial cancer;Developmental Biology;CDO in myogenesis;Myogenesis;TGF_beta_Receptor
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.502
- rvis_EVS
- -0.64
- rvis_percentile_EVS
- 16.63
Haploinsufficiency Scores
- pHI
- 0.392
- hipred
- Y
- hipred_score
- 0.777
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.275
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctnna2
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); reproductive system 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); hearing/vestibular/ear phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- cytoskeleton organization;axonogenesis;radial glia guided migration of Purkinje cell;dendrite morphogenesis;brain morphogenesis;positive regulation of muscle cell differentiation;regulation of synapse structural plasticity;prepulse inhibition;cell-cell adhesion;modification of postsynaptic actin cytoskeleton
- Cellular component
- nucleus;cytoplasm;cytosol;adherens junction;cell-cell adherens junction;actin cytoskeleton;basolateral plasma membrane;lamellipodium;axon;hippocampal mossy fiber to CA3 synapse;parallel fiber to Purkinje cell synapse;presynaptic active zone cytoplasmic component;extrinsic component of presynaptic membrane;extrinsic component of postsynaptic membrane;postsynaptic density, intracellular component
- Molecular function
- structural constituent of cytoskeleton;protein binding;identical protein binding;cadherin binding;actin filament binding