CTNNA2 (catenin alpha 2)

Gene

• Entrez ID: 1496
• Gene name: Catenin alpha 2
• Gene symbol: CTNNA2
• Synonyms (NCBI Gene): CAP-R, CAPR, CDCBM9, CT114, CTNR
• Chromosome: 2
• Chromosome location: 2p12

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs760139097	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, 3 prime UTR variant
rs778294237	C>T	Pathogenic	Coding sequence variant, stop gained
rs1413537928	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT914920	hsa-miR-548p	CLIP-seq
MIRT914921	hsa-miR-3646	CLIP-seq
MIRT914922	hsa-miR-3662	CLIP-seq
MIRT914923	hsa-miR-451b	CLIP-seq
MIRT914924	hsa-miR-509-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005198	Function	Structural molecule activity	IEA
GO:0005200	Function	Structural constituent of cytoskeleton	NAS	8432524
GO:0005515	Function	Protein binding	IPI	16182284, 17679699, 33961781, 36950384
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	16182284
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005912	Component	Adherens junction	IBA
GO:0005912	Component	Adherens junction	IEA
GO:0005912	Component	Adherens junction	ISS
GO:0007010	Process	Cytoskeleton organization	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007409	Process	Axonogenesis	IEA
GO:0007409	Process	Axonogenesis	ISS
GO:0008013	Function	Beta-catenin binding	IBA
GO:0010975	Process	Regulation of neuron projection development	IMP	30013181
GO:0014069	Component	Postsynaptic density	IEA
GO:0015629	Component	Actin cytoskeleton	IEA
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0016342	Component	Catenin complex	IBA
GO:0016477	Process	Cell migration	IBA
GO:0021942	Process	Radial glia guided migration of Purkinje cell	IEA
GO:0021942	Process	Radial glia guided migration of Purkinje cell	ISS
GO:0030027	Component	Lamellipodium	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030424	Component	Axon	IEA
GO:0030424	Component	Axon	ISS
GO:0034316	Process	Negative regulation of Arp2/3 complex-mediated actin nucleation	IMP	30013181
GO:0042802	Function	Identical protein binding	IEA
GO:0042995	Component	Cell projection	IEA
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0045296	Function	Cadherin binding	IEA
GO:0048813	Process	Dendrite morphogenesis	IEA
GO:0048813	Process	Dendrite morphogenesis	ISS
GO:0048854	Process	Brain morphogenesis	IEA
GO:0048854	Process	Brain morphogenesis	ISS
GO:0051015	Function	Actin filament binding	IBA
GO:0051015	Function	Actin filament binding	IDA	30013181
GO:0051015	Function	Actin filament binding	IEA
GO:0051823	Process	Regulation of synapse structural plasticity	IEA
GO:0051823	Process	Regulation of synapse structural plasticity	ISS
GO:0060134	Process	Prepulse inhibition	IEA
GO:0060134	Process	Prepulse inhibition	ISS
GO:0070161	Component	Anchoring junction	IEA
GO:0098609	Process	Cell-cell adhesion	IBA
GO:0098609	Process	Cell-cell adhesion	ISS
GO:0098686	Component	Hippocampal mossy fiber to CA3 synapse	IEA
GO:0098688	Component	Parallel fiber to Purkinje cell synapse	IEA
GO:0098831	Component	Presynaptic active zone cytoplasmic component	IEA
GO:0098885	Process	Modification of postsynaptic actin cytoskeleton	IEA
GO:0098888	Component	Extrinsic component of presynaptic membrane	IEA
GO:0098890	Component	Extrinsic component of postsynaptic membrane	IEA
GO:0099092	Component	Postsynaptic density, intracellular component	IEA
GO:2001222	Process	Regulation of neuron migration	IMP	30013181

Other IDs

• MIM: 114025
• HGNC: 2510
• e!Ensembl: ENSG00000066032

Protein

• UniProt ID: P26232
• Protein name: Catenin alpha-2 (Alpha N-catenin) (Alpha-catenin-related protein)
• Protein function: May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system (By similarity). Required for proper regulation of cortical neuronal migration and neurite
• PDB: 6DUW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01044	Vinculin	18 → 337	Vinculin family	Family
  PF01044	Vinculin	331 → 914	Vinculin family	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in neural tissues, with strongest expression in fetal and adult brain. Expressed in the developing cortical plate and marginal zone of 20-week-old human fetal brain. {ECO:0000269|PubMed:30013181}.
• Sequence:

  MTSATSPIILKWDPKSLEIRTLTVERLLEPLVTQVTTLVNTSNKGPSGKKKGRSKKAHVL
  AASVEQATQNFLEKGEQIAKESQDLKEELVAAVEDVRKQGETMRIASSEFADDPCSSVKR
  GTMVRAARALLSAVTRLLILADMADVMRLLSHLKIVEEALEAVKNATNEQDLANRFKEFG
  KEMVKLNYVAARRQQELKDPHCRDEMAAARGALKKNATMLYTASQAFLRHPDVAATRANR
  DYVFKQVQEAIAGISNAAQATSPTDEAKGHTGIGELAAALNEFDNKIILDPMTFSEARFR
  PSLEERLESIISGAALMADSSCTRDDRRERIVAECNAVRQALQDLLSEYMNNTGRKEKGD
  PLNIAIDKMTKKTRDLRRQLRKAVMDHISDSFLETNVPLLVLIEAAKSGNEKEVKEYAQV
  FREHANKLVEVANLACSISNNEEGVKLVRMAATQIDSLCPQVINAALTLAARPQSKVAQD
  NMDVFKDQWEKQVRVLTEAVDDITSVDDFLSVSENHILEDVNKCVIALQEGDVDTLDRTA
  GAIRGRAARVIHIINAEMENYEAGVYTEKVLEATKLLSETVMPRFAEQVEVAIEALSANV
  PQPFEENEFIDASRLVYDGVRDIRKAVLMIRTPEELEDDSDFEQEDYDVRSRTSVQTEDD
  QLIAGQSARAIMAQLPQEEKAKIAEQVEIFHQEKSKLDAEVAKWDDSGNDIIVLAKQMCM
  IMMEMTDFTRGKGPLKNTSDVINAAKKIAEAGSRMDKLARAVADQCPDSACKQDLLAYLQ
  RIALYCHQLNICSKVKAEVQNLGGELIVSGTGVQSTFTTFYEVDCDVIDGGRASQLSTHL
  PTCAEGAPIGSGSSDSSMLDSATSLIQAAKNLMNAVVLTVKASYVASTKYQKVYGTAAVN
  SPVVSWKMKAPEKKPLVKREKPEEFQTRVRRGSQKKHISPVQALSEFKAMDSF

• Sequence length: 953

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cortical dysplasia, complex, with other brain malformations 9	Likely pathogenic; Pathogenic	rs2467103861, rs2468044149, rs760139097, rs1413537928, rs778294237	RCV003333419 RCV003404955 RCV000721107 RCV000721108 RCV000721109	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary breast ovarian cancer syndrome	Pathogenic	rs2104990962	RCV001374517	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOPIC ECZEMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CTNNA2-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EARLY-ONSET ALZHEIMERS DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LISSENCEPHALY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACROGYRIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN SEROUS CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPROSTHETIC OSTEOLYSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKIN CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKIN NEOPLASM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STOMACH NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTERINE FIBROID	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Agyria	Agyria	CTD_human_DG	30013181		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	22881374, 33797837	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Alzheimer Disease, Late Onset	Alzheimer disease	BEFREE	22881374		★☆☆☆☆ Found in Text Mining only
Alzheimer`s Disease	Alzheimer disease	GWASDB_DG	23535033		★☆☆☆☆ Found in Text Mining only
Alzheimer`s Disease	Alzheimer disease	GWASCAT_DG	23535033		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	39999946	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bladder Neoplasm	Bladder Neoplasm	BEFREE	29928337		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	GWASCAT_DG	25824743		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	25824743	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	24100690		★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	29928337		★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	28679692	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 9	Cortical Dysplasia With Other Brain Malformations	GENOMICS_ENGLAND_DG	30013181		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 9	Cortical Dysplasia With Other Brain Malformations	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	23552671, 37680885	Associate	★☆☆☆☆ Found in Text Mining only
Disruptive Impulse Control and Conduct Disorders	Disruptive, impulse control, and conduct disorders	Pubtator	27167163	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	30526004		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	30526004		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	30013181		★☆☆☆☆ Found in Text Mining only
Hereditary Diffuse Gastric Cancer	Gastric Cancer	CTD_human_DG	24816253		★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	30013181		★☆☆☆☆ Found in Text Mining only
Laryngeal Neoplasms	Laryngeal neoplasm	Pubtator	24100690	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	CTD_human_DG	30013181		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lissencephaly	Lissencephaly	BEFREE	31585108		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	30526004		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	CTD_human_DG	24816253		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	29928337		★☆☆☆☆ Found in Text Mining only
Mantle cell lymphoma	Mantle Cell Lymphoma	BEFREE	30409719		★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	GWASDB_DG	19629137		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24100690, 31489113		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	31489113		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	37800791	Associate	★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	BEFREE	30013181		★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	CTD_human_DG	30013181		★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	18163523		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	18163523		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	GWASCAT_DG	29730043		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	39999946	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Severe intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic Quadriplegia	Spastic Quadriplegia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	24100690	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	24100690		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	CTD_human_DG	24816253		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	37800791	Associate	★☆☆☆☆ Found in Text Mining only