CTNNA2 catenin alpha 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CTNNA2provided by HGNC
Official Full Name: catenin alpha 2provided by HGNC
Primary source: HGNC:HGNC:2510
See related: Ensembl:ENSG00000066032 MIM:114025; AllianceGenome:HGNC:2510
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CAPR; CTNR; CAP-R; CT114; CDCBM9
Summary: Enables actin filament binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation; regulation of neuron migration; and regulation of neuron projection development. Located in cytoplasm. Implicated in complex cortical dysplasia with other brain malformations. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in brain (RPKM 26.7), testis (RPKM 6.2) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 2p12

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (79185377..80648780)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (79185703..80649017)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (79412503..80875905)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel-miR-4885 can bind to 3' untranslated region of CTNNA2 to reduce cell adhesion.
Title: Novel-miR-4885 Promotes Migration and Invasion of Esophageal Cancer Cells Through Targeting CTNNA2.
Single nucleotide polymorphisms in CTNNA2 show associations in Schizophrenia and general cognitive function.
Title: Identification of Genetic Loci Jointly Influencing Schizophrenia Risk and the Cognitive Traits of Verbal-Numerical Reasoning, Reaction Time, and General Cognitive Function.
One association in the CTNNA2 gene on chromosome 2p12 [rs1567532, hazard ratio (HR) = 1.75, 95% confidence interval (CI) 1.19-2.58, P = 0.005 for homozygotes for the minor allele] and one in the last intron of the RUNX2 gene on chromosome 6p21 (rs12209785, HR = 0.88, 95% CI 0.80-0.98, P = 0.014 for heterozygotes) are of particular relevance. These loci do not coincide with those that showed the strongest associations in t
Title: Association of genetic polymorphisms with survival of pancreatic ductal adenocarcinoma patients.
SNP 50-kb upstream from CTNNA2 was associated with impulsivity in Native American sample.
Title: Single nucleotide polymorphisms in the REG-CTNNA2 region of chromosome 2 and NEIL3 associated with impulsivity in a Native American sample.
Single nucleotide polymorphism in CTNNA2 is associated with breast cancer susceptibility.
Title: A pilot genome-wide association study of breast cancer susceptibility loci in Indonesia.
CTNNA2 gene increases the risk of alcohol addiction in White women.
Title: TARV: tree-based analysis of rare variants identifying risk modifying variants in CTNNA2 and CNTNAP2 for alcohol addiction.
CTNNA2 and CTNNA3 are tumor suppressor genes frequently mutated in laryngeal carcinomas.
Title: Cell-cell adhesion genes CTNNA2 and CTNNA3 are tumour suppressors frequently mutated in laryngeal carcinomas.
Common variants in CTNNA2 are associated with excitement-seeking and risk-taking.
Title: Meta-analysis of genome-wide association studies identifies common variants in CTNNA2 associated with excitement-seeking.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cortical dysplasia, complex, with other brain malformations 9 MedGen: C4748540 OMIM: 618174 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs). EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of orthostatic hypotension and supine-standing blood pressure changes in two korean populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope transmembrane glycoprotein gp41	env	HIV-1 gp41 and alpha-catenin co-localize in gp160 and GST-alpha-catenin expressing cells; the leucine zipper-like domain (gp160 residues 791-824) of gp41 interacts strongly with the carboxy terminus (residues 795-906) of alpha-catenin	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48071 (e-PCR)
- UniSTS:4612

D2S2191 (e-PCR), detects polymorphism
- UniSTS:65285

1886 (e-PCR)
- UniSTS:13076

SHGC-79646 (e-PCR)
- UniSTS:101403

SHGC-83284 (e-PCR)
- UniSTS:101162

SHGC-107219 (e-PCR)
- UniSTS:170284

SHGC-17687 (e-PCR)
- UniSTS:46130

Cda0zh07 (e-PCR)
- UniSTS:55863

SHGC-105309 (e-PCR)
- UniSTS:169276

RH123366 (e-PCR)
- UniSTS:135742

RH120192 (e-PCR)
- UniSTS:133184

SHGC-79114 (e-PCR)
- UniSTS:95811

RH47921 (e-PCR)
- UniSTS:52291

RH102250 (e-PCR)
- UniSTS:96584

WI-7682 (e-PCR)
- UniSTS:52048

D2S2082 (e-PCR)
- UniSTS:76384

GDB:315061 (e-PCR)
- UniSTS:156512

WI-18395 (e-PCR)
- UniSTS:68965

STS-M78331 (e-PCR)
- UniSTS:62322

SHGC-153496 (e-PCR)
- UniSTS:177784

RH66010 (e-PCR)
- UniSTS:89466

D2S253 (e-PCR), detects polymorphism
- UniSTS:5755

D2S1942E (e-PCR)
- UniSTS:153725

D2S195E (e-PCR)
- UniSTS:49546

SHGC-58461 (e-PCR)
- UniSTS:94347

CTNNA2_567 (e-PCR)
- UniSTS:468364

D2S2508 (e-PCR)
- UniSTS:80795

SHGC-172957 (e-PCR)
- UniSTS:183462

RH123973 (e-PCR)
- UniSTS:136111

G63245 (e-PCR)
- UniSTS:140214

D2S2180 (e-PCR), detects polymorphism
- UniSTS:30147

SHGC-147872 (e-PCR)
- UniSTS:176067

SHGC-31140 (e-PCR)
- UniSTS:23756

D2S1708E (e-PCR)
- UniSTS:150737

G10614 (e-PCR)
- UniSTS:63953

D2S139 (e-PCR), detects polymorphism
- UniSTS:13780

G59621 (e-PCR)
- UniSTS:136924

SHGC-142093 (e-PCR)
- UniSTS:171245

D2S139 (e-PCR), detects polymorphism
- UniSTS:55533

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin filament binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural constituent of cytoskeleton	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in axonogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in dendrite morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of Arp2/3 complex-mediated actin nucleation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in prepulse inhibition	ISS Inferred from Sequence or Structural Similarity more info
involved_in radial glia guided migration of Purkinje cell	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse structural plasticity	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IEA Inferred from Electronic Annotation more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	ISS Inferred from Sequence or Structural Similarity more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: catenin alpha-2

Names: alpha-N-catenin; alpha-catenin-related protein; cadherin-associated protein, related; cancer/testis antigen 114; catenin (cadherin-associated protein), alpha 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001164883.2 → NP_001158355.1 catenin alpha-2 isoform 2

See identical proteins and their annotated locations for NP_001158355.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two consecutive exons in the 3' coding region but maintains the reading frame compared to variant 1. The resulting isoform (2) lacks an internal segment near the C-terminus compared to isoform 3.

Source sequence(s)

AK295181, BC052996, DA313393

Consensus CDS

CCDS54371.1

UniProtKB/Swiss-Prot

P26232

Related

ENSP00000486160.1, ENST00000629316.2

Conserved Domains (1) summary

pfam01044
Location:81 → 821

Vinculin; Vinculin family
NM_001282597.3 → NP_001269526.1 catenin alpha-2 isoform 3

See identical proteins and their annotated locations for NP_001269526.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) encodes the longest isoform (3).

Source sequence(s)

AC008067, AC010975, AC011741, AC011746, AC096573, AC096753, AC104780, FJ695201

Consensus CDS

CCDS62944.1

UniProtKB/Swiss-Prot

B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0

Related

ENSP00000384638.4, ENST00000402739.9

Conserved Domains (1) summary

pfam01044
Location:81 → 914

Vinculin; Vinculin family
NM_001282598.2 → NP_001269527.1 catenin alpha-2 isoform 4

See identical proteins and their annotated locations for NP_001269527.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) has an alternate 5' terminal exon that includes an upstream in-frame AUG start codon, and lacks an in-frame exon in the 3' coding region, compared to variant 3. The resulting isoform (4) is longer at the N-terminus but lacks an internal segment near the C-terminus compared to isoform 3.

Source sequence(s)

AC010975, AK303035, BC052996

UniProtKB/Swiss-Prot

P26232

Conserved Domains (1) summary

pfam01044
Location:115 → 900

Vinculin; Vinculin family
NM_001282599.2 → NP_001269528.1 catenin alpha-2 isoform 5

See identical proteins and their annotated locations for NP_001269528.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and has multiple coding region differences compared to variant 3. These differences include translation initiation at an alternate AUG start codon. The resulting isoform (5) has a shorter and distinct N-terminus and lacks an internal segment near the C-terminus compared to isoform 3.

Source sequence(s)

BC052996, BX537769

Consensus CDS

CCDS62945.1

UniProtKB/TrEMBL

A0A0A0MRI5

Related

ENSP00000341500.3, ENST00000343114.7

Conserved Domains (1) summary

pfam01044
Location:32 → 545

Vinculin; Vinculin family
NM_001282600.2 → NP_001269529.1 catenin alpha-2 isoform 6

See identical proteins and their annotated locations for NP_001269529.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) has an alternate exon in the 5' UTR and has multiple coding region differences compared to variant 3. These differences include translation initiation at a downstream AUG start codon. The resulting isoform (6) is shorter at the N-terminus and lacks an internal segment near the C-terminus compared to isoform 3.

Source sequence(s)

BC052996, BI599815, HQ589336

Consensus CDS

CCDS74531.1

UniProtKB/TrEMBL

A0A0A0MRI5, F6KRI5

Related

ENSP00000444675.2, ENST00000541047.5

Conserved Domains (1) summary

pfam01044
Location:1 → 498

Vinculin; Vinculin family
NM_001320810.2 → NP_001307739.1 catenin alpha-2 isoform 7

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence compared to variant 3. This difference includes translation initiation at a downstream AUG start codon. The resulting isoform (7) is shorter at the N-terminus compared to isoform 3.

Source sequence(s)

AC008067, BI599815, BX648368, M94151

UniProtKB/TrEMBL

A0A0A0MRI5

Related

ENSP00000355398.5, ENST00000361291.8

Conserved Domains (1) summary

pfam01044
Location:1 → 546

Vinculin; Vinculin family
NM_001399737.1 → NP_001386666.1 catenin alpha-2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (8) lacks an in-frame exon in the 3' coding region compared to variant 3 and differs in the 5' UTR. The resulting isoform (1) lacks an internal segment near the C-terminus compared to isoform 3. Variants 1 and 8 encode the same isoform (1).

Source sequence(s)

AC008067, AC010975, AC011741, AC011746, AC011754, AC018733, AC096573, AC096753, AC104780, FJ695201

Consensus CDS

CCDS42703.2

Related

ENSP00000418191.1, ENST00000466387.5

Conserved Domains (1) summary

pfam01044
Location:81 → 866

Vinculin; Vinculin family
NM_004389.4 → NP_004380.2 catenin alpha-2 isoform 1

See identical proteins and their annotated locations for NP_004380.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region compared to variant 3. The resulting isoform (1) lacks an internal segment near the C-terminus compared to isoform 3. Variants 1 and 8 encode the same isoform (1).

Source sequence(s)

BC040458, BC052996, DA313393

Consensus CDS

CCDS42703.2

UniProtKB/Swiss-Prot

P26232

UniProtKB/TrEMBL

Q49AD3

Related

ENSP00000419295.1, ENST00000496558.5

Conserved Domains (1) summary

pfam01044
Location:81 → 866

Vinculin; Vinculin family