ATXN2 ataxin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATXN2provided by HGNC
Official Full Name: ataxin 2provided by HGNC
Primary source: HGNC:HGNC:10555
See related: Ensembl:ENSG00000204842 MIM:601517; AllianceGenome:HGNC:10555
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: mouse all
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Genomic context

Location:: 12q24.12

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (111452214..111599673, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (111432772..111576594, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (111890018..112037477, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Abnormal open states patterns in the ATXN2 DNA sequence depends on the CAG repeats length.
Title: Abnormal open states patterns in the ATXN2 DNA sequence depends on the CAG repeats length.
Concerted action of ataxin-2 and PABPC1-bound mRNA poly(A) tail in the formation of stress granules.
Title: Concerted action of ataxin-2 and PABPC1-bound mRNA poly(A) tail in the formation of stress granules.
Clinical features, disease progression, and nuclear imaging in ATXN2-related parkinsonism in a longitudinal cohort.
Title: Clinical features, disease progression, and nuclear imaging in ATXN2-related parkinsonism in a longitudinal cohort.
Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation.
Title: Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation.
ATXN2 is a target of N-terminal proteolysis.
Title: ATXN2 is a target of N-terminal proteolysis.
ATXN2-Mediated PI3K/AKT Activation Confers Gastric Cancer Chemoresistance and Attenuates CD8(+) T Cell Cytotoxicity.
Title: ATXN2-Mediated PI3K/AKT Activation Confers Gastric Cancer Chemoresistance and Attenuates CD8(+) T Cell Cytotoxicity.
ATXN2 intermediate expansions in amyotrophic lateral sclerosis.
Title: ATXN2 intermediate expansions in amyotrophic lateral sclerosis.
ATXN2-mediated translation of TNFR1 promotes esophageal squamous cell carcinoma via m(6)A-dependent manner.
Title: ATXN2-mediated translation of TNFR1 promotes esophageal squamous cell carcinoma via m(6)A-dependent manner.
VNTR (CAG)n polymorphism of the ATXN2 gene and metabolic parameters of cardiovascular risk associated with the degree of obesity in the Amerindian population of Oaxaca.
Title: VNTR (CAG)n polymorphism of the ATXN2 gene and metabolic parameters of cardiovascular risk associated with the degree of obesity in the Amerindian population of Oaxaca.
Spinocerebellar ataxia type 2 from an evolutionary perspective: Systematic review and meta-analysis.
Title: Spinocerebellar ataxia type 2 from an evolutionary perspective: Systematic review and meta-analysis.

Submit: New GeneRIF Correction See all GeneRIFs (137)

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
Parkinson disease, late-onset MedGen: C3160718 OMIM: 168600 GeneReviews: Parkinson Disease Overview, Gaucher Disease	not available
Spinocerebellar ataxia type 2 MedGen: C0752121 OMIM: 183090 GeneReviews: Hereditary Ataxia Overview, Spinocerebellar Ataxia Type 2	not available

EBI GWAS Catalog

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_2373-2374:991932707:1 (e-PCR)
- UniSTS:230916

D12S1959 (e-PCR)
- UniSTS:29958

STS-Y08262 (e-PCR)
- UniSTS:24588

MARC_17487-17488:1030377680:1 (e-PCR)
- UniSTS:268316

SHGC-104734 (e-PCR)
- UniSTS:168996

RH70110 (e-PCR)
- UniSTS:41044

SHGC-68495 (e-PCR)
- UniSTS:170077

D12S1672 (e-PCR)
- UniSTS:18308

SHGC-63004 (e-PCR)
- UniSTS:95386

D12S1390E (e-PCR)
- UniSTS:153780

G64274 (e-PCR)
- UniSTS:158653

SGC44303 (e-PCR)
- UniSTS:27085

STS-N24020 (e-PCR)
- UniSTS:61665

Sca2 (e-PCR), detects polymorphism
- UniSTS:144370

Atxn2 (e-PCR), detects polymorphism
- UniSTS:144371

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA 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 mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
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
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
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 more info	PubMed
located_in perinuclear region of cytoplasm	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

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Preferred Names: ataxin-2

Names: spinocerebellar ataxia type 2 protein; trinucleotide repeat-containing gene 13 protein

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

NG_011572.3 RefSeqGene

Range

5362..152463

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_864

mRNA and Protein(s)

NM_001310121.1 → NP_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:144 → 205

LsmAD; LsmAD domain

pfam14438
Location:3 → 76

SM-ATX; Ataxin 2 SM domain

cl26386
Location:303 → 494

DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

cl26464
Location:664 → 988

Atrophin-1; Atrophin-1 family
NM_001310123.1 → NP_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/TrEMBL

Q2M2R5

Related

ENSP00000439338.1, ENST00000535949.5

Conserved Domains (4) summary

pfam06741
Location:120 → 181

LsmAD; LsmAD domain

cl00259
Location:12 → 52

Sm_like; Sm and related proteins

cl25764
Location:641 → 829

PAT1; Topoisomerase II-associated protein PAT1

cl26464
Location:316 → 864

Atrophin-1; Atrophin-1 family
NM_001372574.1 → NP_001359503.1 ataxin-2 isoform 4

Status: REVIEWED

Source sequence(s)

AC002395, AC137055

Consensus CDS

CCDS91750.1

UniProtKB/TrEMBL

A0A5F9ZI57, Q2M2R5

Related

ENSP00000500925.1, ENST00000673436.1

Conserved Domains (6) summary

PHA03247
Location:769 → 1087

PHA03247; large tegument protein UL36; Provisional

COG5180
Location:194 → 339

PBP1; PAB1-binding protein PBP1, interacts with poly(A)-binding protein [RNA processing and modification]

PRK12323
Location:408 → 599

PRK12323; DNA polymerase III subunit gamma/tau

pfam07145
Location:750 → 765

PAM2; Ataxin-2 C-terminal region

pfam06741
Location:249 → 310

LsmAD; LsmAD domain

pfam14438
Location:105 → 181

SM-ATX; Ataxin 2 SM domain
NM_002973.4 → NP_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

CCDS31902.2

UniProtKB/TrEMBL

Q2M2R5, V9GY86

Related

ENSP00000500649.1, ENST00000672613.1

Conserved Domains (6) summary

PHA03247
Location:769 → 1085

PHA03247; large tegument protein UL36; Provisional

COG5180
Location:194 → 339

PBP1; PAB1-binding protein PBP1, interacts with poly(A)-binding protein [RNA processing and modification]

PRK12323
Location:408 → 599

PRK12323; DNA polymerase III subunits gamma and tau; Provisional

pfam06741
Location:249 → 316

LsmAD; LsmAD domain

pfam07145
Location:750 → 765

PAM2; Ataxin-2 C-terminal region

pfam14438
Location:105 → 181

SM-ATX; Ataxin 2 SM domain

RNA

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