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CTNNA3 catenin alpha 3 [ Homo sapiens (human) ]

Gene ID: 29119, updated on 7-Apr-2024

Summary

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Official Symbol
CTNNA3provided by HGNC
Official Full Name
catenin alpha 3provided by HGNC
Primary source
HGNC:HGNC:2511
See related
Ensembl:ENSG00000183230 MIM:607667; AllianceGenome:HGNC:2511
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VR22; ARVD13
Summary
This gene encodes a protein that belongs to the vinculin/alpha-catenin family. The encoded protein plays a role in cell-cell adhesion in muscle cells. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia, familial 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression
Biased expression in heart (RPKM 5.0), brain (RPKM 1.3) and 5 other tissues See more
Orthologs
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Genomic context

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Location:
10q21.3
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (65912523..67763594, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (66775664..68632045, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (67672281..69455953, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378337 Neighboring gene MPRA-validated peak984 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:67374664-67375863 Neighboring gene long intergenic non-protein coding RNA 1515 Neighboring gene uncharacterized LOC105378339 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15172 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15180 Neighboring gene uncharacterized LOC105378340 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15277 Neighboring gene uncharacterized LOC124902440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15319 Neighboring gene uncharacterized LOC124902441 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15324 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15354 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:68197862-68199061 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15439 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15446 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15534 Neighboring gene uncharacterized LOC101928961 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:68685181-68686037 Neighboring gene leucine rich repeat transmembrane neuronal 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:68990733-68991316 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:68990147-68990732 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15618 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15623 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15629 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:69087266-69087766 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15668 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15678 Neighboring gene ribosomal protein L7a pseudogene 51 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15830 Neighboring gene microRNA 7151 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15959 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3449 Neighboring gene Sharpr-MPRA regulatory region 10071 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3455 Neighboring gene tRNA-Ser (anticodon TGA) 1-1 Neighboring gene aldo-keto reductase family 1 member B10 pseudogene 1 Neighboring gene ribosomal protein L21 pseudogene 92

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Proteomics and phosphoproteomics of failing human left ventricle identifies dilated cardiomyopathy-associated phosphorylation of CTNNA3. Reitz CJ, et al. Proc Natl Acad Sci U S A, 2023 May 9. PMID 37126683, Free PMC Article
  2. CTNNA3 genetic polymorphism may be a new genetic signal of type 2 diabetes in the Chinese Han population: a case control study. Zhang Y, et al. BMC Med Genomics, 2021 Oct 30. PMID 34717601, Free PMC Article
  3. Molecular Analysis of Hybrid Neurofibroma/Schwannoma Identifies Common Monosomy 22 and α-T-Catenin/CTNNA3 as a Novel Candidate Tumor Suppressor. Stahn V, et al. Am J Pathol, 2016 Dec. PMID 27765635
  4. Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway. Cocchi E, et al. BMC Psychiatry, 2016 Apr 18. PMID 27091189, Free PMC Article
  5. Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders. Nava C, et al. Eur J Hum Genet, 2014 Jan. PMID 23632794, Free PMC Article

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Proteomics and phosphoproteomics of failing human left ventricle identifies dilated cardiomyopathy-associated phosphorylation of CTNNA3.
    Title: Proteomics and phosphoproteomics of failing human left ventricle identifies dilated cardiomyopathy-associated phosphorylation of CTNNA3.
  2. CTNNA3 genetic polymorphism may be a new genetic signal of type 2 diabetes in the Chinese Han population: a case control study.
    Title: CTNNA3 genetic polymorphism may be a new genetic signal of type 2 diabetes in the Chinese Han population: a case control study.
  3. G allele of rs7903491 in CTNNA3 is a risk factor for essential tremor in Chinese population.
    Title: Assessment of Three New Loci from Genome-wide Association Study in Essential Tremor in Chinese population.
  4. Double MYH7 CTTNA3 heterozygotes showed a variable clinical expression of arrhythmogenic cardiomyopathy and hypertrophic cardiomyopathy. One carrier of double mutations in CTTNA3 and MYH7 genes did not fulfill the current diagnostic criteria for cardiomyopathy.
    Title: Co-inheritance of mutations associated with arrhythmogenic cardiomyopathy and hypertrophic cardiomyopathy.
  5. The functional investigations might indicate involvement of alpha-T-catenin/CTNNA3 in the biology of peripheral nerve sheath tumors.
    Title: Molecular Analysis of Hybrid Neurofibroma/Schwannoma Identifies Common Monosomy 22 and α-T-Catenin/CTNNA3 as a Novel Candidate Tumor Suppressor.
  6. CTNNA3 association with essential tremor.
    Title: Genome-wide association study in essential tremor identifies three new loci.
  7. We conducted a meta-analysis of studies involving CHAT, TFAM, and VR22 polymorphisms and Alzheimer disease susceptibility. For TFAM and VR22, no significant association was detected in studied single-nucleotide polymorphisms (SNPs). Rs10997691 and rs7070570 of VR22 are not significantly associated with AD risk.
    Title: Polymorphisms of CHAT but not TFAM or VR22 are Associated with Alzheimer Disease Risk.
  8. Loss of CTNNA3 expression is associated with hepatocellular carcinoma.
    Title: CTNNA3 is a tumor suppressor in hepatocellular carcinomas and is inhibited by miR-425.
  9. Among the genes replicated across the two samples (permutated p < 0.05 in both of them), CTNNA3 appeared promising. The inorganic cation transmembrane transporter activity pathway (GO:0022890) was associated with antidepressant response in both samples (p = 2.9e-5 and p = 0.001 in the Korean and STAR*D samples, respectively)
    Title: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway.
  10. Two African-ancestry specific variants were found to be significantly associated with metabolic syndrome S: SNP rs73989312[A] near CA10 that conferred increased risk; and SNP rs77244975[C] in CTNNA3 that conferred protection against this disease.
    Title: Genome-wide association study identifies African-ancestry specific variants for metabolic syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (42)

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
Arrhythmogenic right ventricular dysplasia 13
MedGen: C3810138 OMIM: 615616 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-10-24)

ClinGen Genome Curation PagePubMed
Haploinsufficency

No evidence available (Last evaluated 2018-10-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
EBI GWAS Catalog
Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis.
EBI GWAS Catalog
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.
EBI GWAS Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
EBI GWAS Catalog
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
EBI GWAS Catalog
Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.
EBI GWAS Catalog
GWAS of dental caries patterns in the permanent dentition.
EBI GWAS Catalog
Novel genes identified in a high-density genome wide association study for nicotine dependence.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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
nucleocapsid gag HIV-1 NC is identified to have a physical interaction with catenin (cadherin-associated protein), alpha 3 (CTNNA3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC26194, MGC75041

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables beta-catenin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables beta-catenin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables cadherin binding TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in bundle of His cell-Purkinje myocyte adhesion involved in cell communication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IPI
Inferred from Physical Interaction
more info
 PubMed 
involved_in regulation of heart rate by cardiac conduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of ventricular cardiac muscle cell action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in desmosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in fascia adherens IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in fascia adherens IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lamellipodium IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
catenin alpha-3
Names
alpha-T-catenin
alpha-catenin-like protein
catenin (cadherin-associated protein), alpha 3

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.

Genomic

  1. NG_034072.2 RefSeqGene

    Range
    72399..1856071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127384.3 → NP_001120856.1  catenin alpha-3 isoform a

    See identical proteins and their annotated locations for NP_001120856.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform a).
    Source sequence(s)
    AC018979, AK289756, AL731538, BC030646, BX103986
    Consensus CDS
    CCDS7269.1
    UniProtKB/Swiss-Prot
    Q5VSR2, Q6P056, Q9UI47
    UniProtKB/TrEMBL
    A8K141
    Related
    ENSP00000508047.1, ENST00000682758.1
    Conserved Domains (1) summary
    pfam01044
    Location:83 → 856
    Vinculin; Vinculin family

  2. NM_001291133.2 → NP_001278062.1  catenin alpha-3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences compared to variant 1. These differences result in distinct 5' and 3' UTRs and cause translation initiation at an alternate start codon compared to variant 1. The encoded protein (isoform b) has a longer N-terminus, a distinct C-terminus, and is shorter compared to isoform a.
    Source sequence(s)
    AC022401, AC026394, BC030646
    UniProtKB/TrEMBL
    Q8WW10
    Conserved Domains (1) summary
    pfam01044
    Location:95 → 369
    Vinculin; Vinculin family

  3. NM_013266.4 → NP_037398.2  catenin alpha-3 isoform a

    See identical proteins and their annotated locations for NP_037398.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC018979, AF091606, AK313882, AL607022, BX103986
    Consensus CDS
    CCDS7269.1
    UniProtKB/Swiss-Prot
    Q5VSR2, Q6P056, Q9UI47
    UniProtKB/TrEMBL
    A8K141
    Related
    ENSP00000389714.1, ENST00000433211.7
    Conserved Domains (1) summary
    pfam01044
    Location:83 → 856
    Vinculin; Vinculin family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    65912523..67763594 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047425124.1 → XP_047281080.1  catenin alpha-3 isoform X3

  2. XM_017016152.2 → XP_016871641.1  catenin alpha-3 isoform X2

    UniProtKB/TrEMBL
    A8K141

  3. XM_017016151.2 → XP_016871640.1  catenin alpha-3 isoform X1

    UniProtKB/TrEMBL
    A8K141

  4. XM_017016155.3 → XP_016871644.1  catenin alpha-3 isoform X4

  5. XM_017016156.2 → XP_016871645.1  catenin alpha-3 isoform X4

  6. XM_017016157.3 → XP_016871646.1  catenin alpha-3 isoform X5

  7. XM_017016158.3 → XP_016871647.1  catenin alpha-3 isoform X6

    UniProtKB/TrEMBL
    Q8WW10
    Conserved Domains (1) summary
    pfam01044
    Location:95 → 369
    Vinculin; Vinculin family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    66775664..68632045 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054365669.1 → XP_054221644.1  catenin alpha-3 isoform X3

  2. XM_054365668.1 → XP_054221643.1  catenin alpha-3 isoform X2

  3. XM_054365667.1 → XP_054221642.1  catenin alpha-3 isoform X1

  4. XM_054365671.1 → XP_054221646.1  catenin alpha-3 isoform X4

  5. XM_054365670.1 → XP_054221645.1  catenin alpha-3 isoform X4

  6. XM_054365672.1 → XP_054221647.1  catenin alpha-3 isoform X5

  7. XM_054365673.1 → XP_054221648.1  catenin alpha-3 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UI47.2 GenPept UniProtKB/Swiss-Prot:Q9UI47

Gene LinkOut

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