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    ATXN2 ataxin 2 [ Homo sapiens (human) ]

    Gene ID: 6311, updated on 5-Dec-2021

    Summary

    Official Symbol
    ATXN2provided by HGNC
    Official Full Name
    ataxin 2provided by HGNC
    Primary source
    HGNC:HGNC:10555
    See related
    Ensembl:ENSG00000204842 MIM:601517
    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
    ATX2; SCA2; TNRC13
    Summary
    This gene belongs to a group of genes that is associated with microsatellite-expansion diseases, a class of neurological and neuromuscular disorders caused by expansion of short stretches of repetitive DNA. The protein encoded by this gene has two globular domains near the N-terminus, one of which contains a clathrin-mediated trans-Golgi signal and an endoplasmic reticulum exit signal. The encoded cytoplasmic protein localizes to the endoplasmic reticulum and plasma membrane, is involved in endocytosis, and modulates mTOR signals, modifying ribosomal translation and mitochondrial function. The N-terminal region of the protein contains a polyglutamine tract of 14-31 residues that can be expanded in the pathogenic state to 32-200 residues. Intermediate length expansions of this tract increase susceptibility to amyotrophic lateral sclerosis, while long expansions of this tract result in spinocerebellar ataxia-2, an autosomal-dominantly inherited, neurodegenerative disorder. Genome-wide association studies indicate that loss-of-function mutations in this gene may be associated with susceptibility to type I diabetes, obesity and hypertension. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
    Expression
    Ubiquitous expression in testis (RPKM 11.3), brain (RPKM 9.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ATXN2 in Genome Data Viewer
    Location:
    12q24.12
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109.20211119 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (111452214..111599673, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111890018..112037477, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2356 Neighboring gene SH2B adaptor protein 3 Neighboring gene IFITM3 pseudogene 5 Neighboring gene ATXN2 antisense RNA Neighboring gene BRCA1 associated protein Neighboring gene PEST containing nuclear protein pseudogene 1 Neighboring gene acyl-CoA dehydrogenase family member 10

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    GeneReviews: Not available
    Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
    GeneReviews: Not available
    Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo.
    GeneReviews: Not available
    Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
    GeneReviews: Not available
    Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin.
    GeneReviews: Not available
    Genome-wide association study identifies eight loci associated with blood pressure.
    GeneReviews: Not available
    Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
    GeneReviews: Not available
    Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease.
    GeneReviews: Not available
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    GeneReviews: Not available
    Multiple common variants for celiac disease influencing immune gene expression.
    GeneReviews: Not available
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    GeneReviews: Not available
    New loci associated with kidney function and chronic kidney disease.
    GeneReviews: Not available
    Newly identified genetic risk variants for celiac disease related to the immune response.
    GeneReviews: Not available
    Novel associations for hypothyroidism include known autoimmune risk loci.
    GeneReviews: Not available
    Parkinson disease, late-onset
    MedGen: C3160718 OMIM: 168600 GeneReviews: Parkinson Disease Overview
    Compare labs
    Seventy-five genetic loci influencing the human red blood cell.
    GeneReviews: Not available
    Spinocerebellar ataxia type 2 Compare labs
    The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of ataxin 2 (ATXN2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ46772

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables epidermal growth factor receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in P-body assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in RNA metabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in RNA transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of translation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in stress granule assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in stress granule assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasmic stress granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane HDA PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of polysome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ataxin-2
    Names
    spinocerebellar ataxia type 2 protein
    trinucleotide repeat-containing gene 13 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_011572.3 RefSeqGene

      Range
      5362..152463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_864

    mRNA and Protein(s)

    1. NM_001310121.1NP_001297050.1  ataxin-2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, uses alternate splice sites in the 5' coding region, which results in use of a downstream start codon, and contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2, which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AA731027, AI668891, BC111757, BM671308
      Consensus CDS
      CCDS81739.1
      UniProtKB/TrEMBL
      F8VQP2, Q2M2R5
      Related
      ENSP00000445583.2, ENST00000542287.6
      Conserved Domains (4) summary
      pfam06741
      Location:144205
      LsmAD; LsmAD domain
      pfam14438
      Location:376
      SM-ATX; Ataxin 2 SM domain
      cl26386
      Location:303494
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
      cl26464
      Location:664988
      Atrophin-1; Atrophin-1 family
    2. NM_001310123.1NP_001297052.1  ataxin-2 isoform 3

      See identical proteins and their annotated locations for NP_001297052.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, one of which results in use of a downstream start codon compared to variant 1. It encodes isoform 3, which has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AA731027, AI668891, BC114546, BM671308
      Consensus CDS
      CCDS81738.1
      UniProtKB/Swiss-Prot
      Q99700
      Related
      ENSP00000439338.1, ENST00000535949.5
      Conserved Domains (4) summary
      pfam06741
      Location:120181
      LsmAD; LsmAD domain
      cl00259
      Location:1252
      Sm_like; Sm and related proteins
      cl25764
      Location:641829
      PAT1; Topoisomerase II-associated protein PAT1
      cl26464
      Location:316864
      Atrophin-1; Atrophin-1 family
    3. NM_001372574.1NP_001359503.1  ataxin-2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC002395, AC137055
      Related
      ENSP00000500925.1, ENST00000673436.1
      Conserved Domains (6) summary
      PHA03247
      Location:7691087
      PHA03247; large tegument protein UL36; Provisional
      COG5180
      Location:194339
      PBP1; PAB1-binding protein PBP1, interacts with poly(A)-binding protein [RNA processing and modification]
      PRK12323
      Location:408599
      PRK12323; DNA polymerase III subunit gamma/tau
      pfam07145
      Location:750765
      PAM2; Ataxin-2 C-terminal region
      pfam06741
      Location:249310
      LsmAD; LsmAD domain
      pfam14438
      Location:105181
      SM-ATX; Ataxin 2 SM domain
    4. NM_002973.4NP_002964.4  ataxin-2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC002395, AC137055
      Consensus CDS
      CCDS31902.1
      Related
      ENSP00000500649.1, ENST00000672613.1
      Conserved Domains (6) summary
      PHA03247
      Location:7691085
      PHA03247; large tegument protein UL36; Provisional
      COG5180
      Location:194339
      PBP1; PAB1-binding protein PBP1, interacts with poly(A)-binding protein [RNA processing and modification]
      PRK12323
      Location:408599
      PRK12323; DNA polymerase III subunits gamma and tau; Provisional
      pfam06741
      Location:249316
      LsmAD; LsmAD domain
      pfam07145
      Location:750765
      PAM2; Ataxin-2 C-terminal region
      pfam14438
      Location:105181
      SM-ATX; Ataxin 2 SM domain

    RNA

    1. NR_132311.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA731027, AC137055, AI668891, DA796951, U70323, Y08262
      Related
      ENST00000483311.6

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

      Range
      111452214..111599673 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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