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ATXN10 ataxin 10 [ Homo sapiens (human) ]

Gene ID: 25814, updated on 11-Apr-2024

Summary

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Official Symbol
ATXN10provided by HGNC
Official Full Name
ataxin 10provided by HGNC
Primary source
HGNC:HGNC:10549
See related
Ensembl:ENSG00000130638 MIM:611150; AllianceGenome:HGNC:10549
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
E46L; ATX10; SCA10; HUMEEP
Summary
This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in brain (RPKM 40.8), thyroid (RPKM 30.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q13.31
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45671834..45845307)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (46156561..46330004)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (46067714..46241187)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373069 Neighboring gene uncharacterized LOC105373067 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:46034441-46035640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13883 Neighboring gene uncharacterized LOC105373068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46044567-46045067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19229 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:46145933-46146130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46153547-46154545 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46158531-46159124 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:46164292-46164865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13887 Neighboring gene microRNA 4762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13888 Neighboring gene origin of replication for ATXN10 repeat region Neighboring gene ataxin 10 repeat instability region Neighboring gene TRNT1 pseudogene 2 Neighboring gene VISTA enhancer hs1559 Neighboring gene uncharacterized LOC105373071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46263223-46263797 Neighboring gene uncharacterized LOC107985535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46275792-46276707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46276708-46277622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46291489-46292372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46292373-46293254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46331075-46331575 Neighboring gene Wnt family member 7B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46358809-46359309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46362863-46363759 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:46364456-46365655

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Clinical and Genetic Evaluation of Spinocerebellar Ataxia Type 10 in 16 Brazilian Families. Domingues BMD, et al. Cerebellum, 2019 Oct. PMID 31377949
  2. ATXN10 Microsatellite Distribution in a Peruvian Amerindian Population. Véliz-Otani D, et al. Cerebellum, 2019 Oct. PMID 31342269
  3. Ataxin-10 is involved in Golgi membrane dynamics. Tian J, et al. J Genet Genomics, 2017 Nov 20. PMID 29169923
  4. Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation. Bampi GB, et al. Neuromolecular Med, 2017 Dec. PMID 28905220
  5. First report of a Japanese family with spinocerebellar ataxia type 10: The second report from Asia after a report from China. Naito H, et al. PLoS One, 2017. PMID 28542277, Free PMC Article

See all (129) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The most common clinical presentation of SCA10 in Brazilian families was pure cerebellar ataxia.
    Title: Clinical and Genetic Evaluation of Spinocerebellar Ataxia Type 10 in 16 Brazilian Families.
  2. ATXN10 allele distribution in a healthy Amerindian population from Peru does not differ from that of other populations.
    Title: ATXN10 Microsatellite Distribution in a Peruvian Amerindian Population.
  3. Ataxin-10 is involved in Golgi membrane dynamics
    Title: Ataxin-10 is involved in Golgi membrane dynamics.
  4. The 19-CGGC-14 shared haplotype was found in 47% of Brazilian and in 63% of Peruvian families. Frequencies from both are statistically different from Brazilian controls but not Quechua controls. The most frequent haplotype in Quechuas, 19-15-CGGC-14-10, is found in 50% of Brazilian and in 65% of Peruvian patients. The ATTCT expansion may have arisen in a Native American chromosome.
    Title: Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation.
  5. Polymorphism in ATXN10 gene is associated with spinocerebellar ataxia type 10.
    Title: First report of a Japanese family with spinocerebellar ataxia type 10: The second report from Asia after a report from China.
  6. Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 expansions of ataxin-10 has been reported.
    Title: Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions.
  7. Single molecule real time sequencing of long tandem nucleotide repeats in spinocerebellar ataxia ATXN10 reveals unique insight of repeat expansion structure in three unrelated patients.
    Title: SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure.
  8. This is the first description of a family with two SCA mutations with affected subjects having a combined SCA2 and SCA10 phenotype.
    Title: Bolivian kindred with combined spinocerebellar ataxia types 2 and 10.
  9. Inhibition of Aurora B or expression of the S12A mutant renders reduced interaction between Ataxin-10 and polo-like kinase 1 (Plk1), a kinase previously identified to regulate Ataxin-10 in cytokinesis.
    Title: Aurora B-dependent phosphorylation of Ataxin-10 promotes the interaction between Ataxin-10 and Plk1 in cytokinesis.
  10. Data suggest precursor mRNA for SCA10 (crystalized using two model AUUCU SCA10 repeats) exhibits the following conformation: the two asymmetric RNA molecules are antiparallel to each other and the interaction is stabilized by multiple hydrogen bonds.
    Title: Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).
Submit: New GeneRIF Correction See all GeneRIFs (28)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ataxin 10 (ATXN10) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ37990

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cilium assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron projection development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cytokinesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centriole ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in ciliary basal body ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in dendrite IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space HDA PubMed 
located_in membrane HDA PubMed 
located_in midbody IDA
Inferred from Direct Assay
more info
 PubMed 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
ataxin-10
Names
brain protein E46 homolog
spinocerebellar ataxia type 10 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

  1. NG_016212.2 RefSeqGene

    Range
    5037..178510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001167621.2 → NP_001161093.1  ataxin-10 isoform 2

    See identical proteins and their annotated locations for NP_001161093.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK095309, AK294348, BC007508, DB548216, R43701
    Consensus CDS
    CCDS54540.1
    UniProtKB/Swiss-Prot
    Q9UBB4
    Related
    ENSP00000370449.4, ENST00000381061.8
    Conserved Domains (1) summary
    pfam09759
    Location:306 → 403
    Atx10homo_assoc; Spinocerebellar ataxia type 10 protein domain

  2. NM_013236.4 → NP_037368.1  ataxin-10 isoform 1

    See identical proteins and their annotated locations for NP_037368.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK095309, BC007508, DB035174, DB548216, R43701
    Consensus CDS
    CCDS14070.1
    UniProtKB/Swiss-Prot
    A6NLC4, B4DG05, O14998, O15009, Q6I9X4, Q9UBB4
    UniProtKB/TrEMBL
    Q7Z524
    Related
    ENSP00000252934.4, ENST00000252934.10
    Conserved Domains (1) summary
    pfam09759
    Location:370 → 467
    Atx10homo_assoc; Spinocerebellar ataxia type 10 protein domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45671834..45845307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441314.1 → XP_047297270.1  ataxin-10 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    46156561..46330004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325488.1 → XP_054181463.1  ataxin-10 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UBB4.1 GenPept UniProtKB/Swiss-Prot:Q9UBB4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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