ATXN1 ataxin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATXN1provided by HGNC
Official Full Name: ataxin 1provided by HGNC
Primary source: HGNC:HGNC:10548
See related: Ensembl:ENSG00000124788 MIM:601556; AllianceGenome:HGNC:10548
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: ATX1; SCA1; D6S504E
Summary: The autosomal dominant cerebellar ataxias (ADCA) are a heterogeneous group of neurodegenerative disorders characterized by progressive degeneration of the cerebellum, brain stem and spinal cord. Clinically, ADCA has been divided into three groups: ADCA types I-III. ADCAI is genetically heterogeneous, with five genetic loci, designated spinocerebellar ataxia (SCA) 1, 2, 3, 4 and 6, being assigned to five different chromosomes. ADCAII, which always presents with retinal degeneration (SCA7), and ADCAIII often referred to as the `pure' cerebellar syndrome (SCA5), are most likely homogeneous disorders. Several SCA genes have been cloned and shown to contain CAG repeats in their coding regions. ADCA is caused by the expansion of the CAG repeats, producing an elongated polyglutamine tract in the corresponding protein. The expanded repeats are variable in size and unstable, usually increasing in size when transmitted to successive generations. The function of the ataxins is not known. This locus has been mapped to chromosome 6, and it has been determined that the diseased allele contains 40-83 CAG repeats, compared to 6-39 in the normal allele, and is associated with spinocerebellar ataxia type 1 (SCA1). Alternative splicing results in multiple transcript variants, with one variant encoding multiple distinct proteins, ATXN1 and Alt-ATXN1, due to the use of overlapping alternate reading frames. [provided by RefSeq, Nov 2017]
Expression: Ubiquitous expression in endometrium (RPKM 6.8), brain (RPKM 6.7) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6p22.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (16299112..16761460, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (16171667..16634155, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (16299343..16761691, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expanded ATXN1 alters transcription and calcium signaling in SCA1 human motor neurons differentiated from induced pluripotent stem cells.
Title: Expanded ATXN1 alters transcription and calcium signaling in SCA1 human motor neurons differentiated from induced pluripotent stem cells.
Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-kappaB-dependent inflammation response.
Title: Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response.
Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-1.
Title: Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-1.
Epigenetic control of ataxin-1 in multiple sclerosis.
Title: Epigenetic control of ataxin-1 in multiple sclerosis.
Identification of the ataxin-1 interaction network and its impact on spinocerebellar ataxia type 1.
Title: Identification of the ataxin-1 interaction network and its impact on spinocerebellar ataxia type 1.
Spinocerebellar Ataxia Type 1 protein Ataxin-1 is signaled to DNA damage by ataxia-telangiectasia mutated kinase.
Title: Spinocerebellar Ataxia Type 1 protein Ataxin-1 is signaled to DNA damage by ataxia-telangiectasia mutated kinase.
A Structural Study of the Cytoplasmic Chaperone Effect of 14-3-3 Proteins on Ataxin-1.
Title: A Structural Study of the Cytoplasmic Chaperone Effect of 14-3-3 Proteins on Ataxin-1.
Detection Methods and Status of CAT Interruption of ATXN1 in Korean Patients With Spinocerebellar Ataxia Type 1.
Title: Detection Methods and Status of CAT Interruption of ATXN1 in Korean Patients With Spinocerebellar Ataxia Type 1.
CAG repeats>/=34 in Ataxin-1 gene are associated with amyotrophic lateral sclerosis in a Brazilian cohort.
Title: CAG repeats ≥ 34 in Ataxin-1 gene are associated with amyotrophic lateral sclerosis in a Brazilian cohort.
Cortical network dysfunction revealed by magnetoencephalography in carriers of spinocerebellar ataxia 1 or 2 mutation.
Title: Cortical network dysfunction revealed by magnetoencephalography in carriers of spinocerebellar ataxia 1 or 2 mutation.

Submit: New GeneRIF Correction See all GeneRIFs (89)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spinocerebellar ataxia type 1 MedGen: C0752120 OMIM: 164400 GeneReviews: Hereditary Ataxia Overview, Spinocerebellar Ataxia Type 1	not available

EBI GWAS Catalog

Description
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of a quantitative disordered gambling trait. EBI GWAS Catalog EBI GWAS CatalogPubMed
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	HIV-1 Vif upregulates the expression of ataxin 1 (ATXN1) in Vif-expression T cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D6S1354 (e-PCR)
- UniSTS:153605

SHGC-146680 (e-PCR)
- UniSTS:175369

STS-AA010260 (e-PCR)
- UniSTS:28430

RH46829 (e-PCR)
- UniSTS:28699

D6S288 (e-PCR), detects polymorphism
- UniSTS:47900

WI-16958 (e-PCR)
- UniSTS:73001

GDB:216047 (e-PCR)
- UniSTS:156207

GDB:216054 (e-PCR)
- UniSTS:156208

WI-19222 (e-PCR)
- UniSTS:35378

1216 (e-PCR)
- UniSTS:73540

PMC109045P1 (e-PCR)
- UniSTS:270151

G62333 (e-PCR)
- UniSTS:139337

SHGC-79186 (e-PCR)
- UniSTS:102730

SHGC-33945 (e-PCR)
- UniSTS:78931

SGC30752 (e-PCR)
- UniSTS:19027

D6S1461 (e-PCR)
- UniSTS:46433

D6S288 (e-PCR), detects polymorphism
- UniSTS:19342

D6S274 (e-PCR), detects polymorphism
- UniSTS:36751

STS-X79204 (e-PCR)
- UniSTS:4499

G15977 (e-PCR)
- UniSTS:70813

D6S2131 (e-PCR)
- UniSTS:49061

GDB:681830 (e-PCR)
- UniSTS:158635

NoName (e-PCR)
- UniSTS:487347

RH71007 (e-PCR)
- UniSTS:32438

RH118967 (e-PCR)
- UniSTS:138935

SCA1_796 (e-PCR)
- UniSTS:277688

RH35931 (e-PCR)
- UniSTS:87992

D6S324E (e-PCR)
- UniSTS:147385

D6S274 (e-PCR), detects polymorphism
- UniSTS:90054

WI-9349 (e-PCR)
- UniSTS:72936

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables poly(G) binding	IDA Inferred from Direct Assay more info	PubMed
enables poly(U) RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA processing	NAS Non-traceable Author Statement more info	PubMed
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear export	IDA Inferred from Direct Assay more info	PubMed
involved_in social behavior	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nuclear inclusion body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: ataxin-1

Names: alternative ataxin1; spinocerebellar ataxia type 1 protein

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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

NG_011571.1 RefSeqGene

Range

5001..467379

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_863

mRNA and Protein(s)

NM_000332.4 → NP_000323.2 ataxin-1 isoform ATXN1

See identical proteins and their annotated locations for NP_000323.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes multiple distinct proteins due to the use of alternative translation initiation codons. The longer 815 aa protein (ATXN1, PMID:23705062) represents the canonical protein, while a shorter protein (Alt-ATXN1, PMID:23705062) that uses a different reading frame has also been described. This RefSeq represents the longer protein, ATXN1. Variant 2 also encodes ATXN1.

Source sequence(s)

AL009031, AL031120, AL034375, AL137003

Consensus CDS

CCDS34342.1

UniProtKB/Swiss-Prot

P54253, Q17S02, Q9UJG2, Q9Y4J1

Related

ENSP00000244769.3, ENST00000244769.8

Conserved Domains (2) summary

smart00536
Location:573 → 688

AXH; domain in Ataxins and HMG containing proteins

pfam12547
Location:415 → 445

ATXN-1_C; Capicua transcriptional repressor modulator
NM_001128164.2 → NP_001121636.1 ataxin-1 isoform ATXN1

See identical proteins and their annotated locations for NP_001121636.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. This variant encodes the same protein represented by the longer protein encoded by variant 1, ATXN1.

Source sequence(s)

AL009031, BC011026, BP365416, X79204

Consensus CDS

CCDS34342.1

UniProtKB/Swiss-Prot

P54253, Q17S02, Q9UJG2, Q9Y4J1

Related

ENSP00000416360.1, ENST00000436367.6

Conserved Domains (2) summary

smart00536
Location:573 → 688

AXH; domain in Ataxins and HMG containing proteins

pfam12547
Location:415 → 445

ATXN-1_C; Capicua transcriptional repressor modulator
NM_001357857.2 → NP_001344786.1 ataxin-1 isoform Alt-ATXN1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes multiple distinct proteins due to the use of alternative translation initiation codons. The longer, 815 aa protein represents the canonical protein, while a shorter 185 aa protein(Alt-ATXN1, PMID:23760502) that uses a different reading frame has also been described. Alt-ATXN1 does not share structural similarity to the ATXN1, but has been shown to interact with the ATXN1. This RefSeq represents the shorter protein, Alt-ATXN1.

Source sequence(s)

AL009031, BC011026, X79204

Consensus CDS

CCDS87367.1

UniProtKB/TrEMBL

A0A2R8YCF3, L0EPB8

Related

ENSP00000493530.1, ENST00000642969.1