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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
    mouse all
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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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