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    ATXN2 ataxin 2 [ Homo sapiens (human) ]

    Gene ID: 6311, updated on 3-Sep-2017
    Official Symbol
    ATXN2provided by HGNC
    Official Full Name
    ataxin 2provided by HGNC
    Primary source
    HGNC:HGNC:10555
    See related
    Ensembl:ENSG00000204842 MIM:601517; Vega:OTTHUMG00000133475
    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]
    Orthologs
    Location:
    12q24.12
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 12 NC_000012.12 (111452214..111599676, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111890018..112037480, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2356 Neighboring gene uncharacterized LOC105369985 Neighboring gene SH2B adaptor protein 3 Neighboring gene interferon induced transmembrane protein 3 pseudogene Neighboring gene BRCA1 associated protein Neighboring gene PEST containing nuclear protein pseudogene 1 Neighboring gene acyl-CoA dehydrogenase family member 10

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    NHGRI GWA Catalog
    Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
    NHGRI GWA Catalog
    Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo.
    NHGRI GWA Catalog
    Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
    NHGRI GWA Catalog
    Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin.
    NHGRI GWA Catalog
    Genome-wide association study identifies eight loci associated with blood pressure.
    NHGRI GWA Catalog
    Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
    NHGRI GWA Catalog
    Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    NHGRI GWA Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    NHGRI GWA Catalog
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    NHGRI GWA Catalog
    New loci associated with kidney function and chronic kidney disease.
    NHGRI GWA Catalog
    Newly identified genetic risk variants for celiac disease related to the immune response.
    NHGRI GWA Catalog
    Novel associations for hypothyroidism include known autoimmune risk loci.
    NHGRI GWA Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    NHGRI GWA Catalog
    The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study.
    NHGRI GWA Catalog

    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

    • EGF/EGFR Signaling Pathway, organism-specific biosystem (from WikiPathways)
      EGF/EGFR Signaling Pathway, organism-specific biosystemEpidermal growth factor receptor (EGFR) also known as ErbB1/HER1 is a member of the ErbB family of receptor tyrosine kinases which also includes ErbB2 (Neu, HER2), ErbB3 (HER3) and ErbB4 (HER4). Sev...
    • Parkinsons Disease Pathway, organism-specific biosystem (from WikiPathways)
      Parkinsons Disease Pathway, organism-specific biosystemMost people with Parkinson's disease have idiopathic Parkinson's disease (having no specific known cause). A small proportion of cases, however, can be attributed to known genetic factors. Mutations ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ46772

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    epidermal growth factor receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA metabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    RNA transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytoplasmic mRNA processing body assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cytoplasmic mRNA processing body assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    regulation of translation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    stress granule assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    polysome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    ataxin-2
    Names
    spinocerebellar ataxia type 2 protein
    trinucleotide repeat-containing gene 13 protein

    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_011572.2 RefSeqGene

      Range
      5001..152463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    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, OTTHUMP00000241638, ENST00000542287.6, OTTHUMT00000404980
      Conserved Domains (3) summary
      pfam06741
      Location:144205
      LsmAD; LsmAD domain
      pfam07145
      Location:644660
      PAM2; Ataxin-2 C-terminal region
      pfam14438
      Location:271
      SM-ATX; Ataxin 2 SM domain
    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, OTTHUMP00000241637, ENST00000535949.5, OTTHUMT00000404979
      Conserved Domains (2) summary
      pfam06741
      Location:120181
      LsmAD; LsmAD domain
      pfam07145
      Location:620636
      PAM2; Ataxin-2 C-terminal region
    3. NM_002973.3NP_002964.3  ataxin-2 isoform 1

      See identical proteins and their annotated locations for NP_002964.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA731027, AL042619, CA389718, U70323, Y08262
      Consensus CDS
      CCDS31902.1
      UniProtKB/Swiss-Prot
      Q99700
      Related
      ENSP00000366843.3, OTTHUMP00000164680, ENST00000377617.7, OTTHUMT00000257351
      Conserved Domains (3) summary
      pfam06741
      Location:409470
      LsmAD; LsmAD domain
      pfam07145
      Location:909925
      PAM2; Ataxin-2 C-terminal region
      pfam14438
      Location:267336
      SM-ATX; Ataxin 2 SM domain

    RNA

    1. NR_132311.1 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
      ENST00000483311.5, OTTHUMT00000257355

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p7 Primary Assembly

      Range
      111452214..111599676 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      111857982..112005420 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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