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ATXN2 ataxin 2 [ Homo sapiens (human) ]

Gene ID: 6311, updated on 7-Oct-2018

Summary

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]
Expression
Ubiquitous expression in testis (RPKM 11.3), brain (RPKM 9.4) and 25 other tissues See more
Orthologs

Genomic context

See ATXN2 in Genome Data Viewer
Location:
12q24.12
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 SH2B adaptor protein 3 Neighboring gene interferon induced transmembrane protein 3 pseudogene 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

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 BioSystems

  • 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 ...

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
RNA binding HDA 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
PubMed 
regulation of translation NAS
Non-traceable Author Statement
more info
PubMed 
stress granule assembly IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
polysome IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
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)

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 (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, OTTHUMP00000241637, ENST00000535949.5, OTTHUMT00000404979
    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_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
    ENST00000483311.6, OTTHUMT00000257355

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

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