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    VPS13A vacuolar protein sorting 13 homolog A (S. cerevisiae) [ Homo sapiens (human) ]

    Gene ID: 23230, updated on 9-Jun-2013
    Official Symbol
    VPS13Aprovided by HGNC
    Official Full Name
    vacuolar protein sorting 13 homolog A (S. cerevisiae)provided by HGNC
    Primary source
    HGNC:1908
    Locus tag
    RP11-498N2.1
    See related
    Ensembl:ENSG00000197969; HPRD:05814; MIM:605978; Vega:OTTHUMG00000020055
    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
    CHAC; CHOREIN
    Summary
    The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
    Location :
    9q21
    Sequence :
    Chromosome: 9; NC_000009.11 (79792361..80032399)
    See VPS13A in Epigenomics, MapViewer

    Chromosome 9 - NC_000009.11Genomic Context describing neighboring genes Neighboring gene replication factor C (activator 1) 5, 36.5kDa pseudogene Neighboring gene ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2 pseudogene 3 Neighboring gene VPS13A antisense RNA 1 Neighboring gene guanine nucleotide binding protein (G protein), alpha 14 Neighboring gene guanine nucleotide binding protein (G protein), q polypeptide

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Choreoacanthocytosis

    Summary from GeneReviews: Chorea-Acanthocytosis Go to GeneReviews

    Disease Characteristics
    Chorea-acanthocytosis (ChAc) is characterized by a progressive movement disorder, cognitive and behavior changes, a myopathy that can be subclinical, and chronic hyperCKemia in serum. Although the disorder is named for acanthocytosis of the red blood cells, this feature is variable. The movement disorder is mostly limb chorea, but some individuals present with parkinsonism. Dystonia is common and affects the oral region and especially the tongue, causing dysarthria and serious dysphagia with resultant weight loss. Habitual tongue and lip biting are characteristic, as well as tongue protrusion dystonia. Progressive cognitive and behavioral changes resemble those in a frontal lobe syndrome. Seizures are observed in almost half of affected individuals and can be the initial manifestation. Myopathy results in progressive distal muscle wasting and weakness. Mean age of onset in ChAc is about 30 years, although ChAc can develop as early as the first decade or as late as the seventh decade. It runs a chronic progressive course and may lead to major disability within a few years. Life expectancy is reduced, with age of death ranging from 28 to 61 years.
    Diagnosis Testing
    The diagnosis of ChAc is based primarily on clinical findings, the presence of characteristic MRI findings, and evidence of muscle disease. CT and MRI reveal atrophy of the caudate nuclei with dilatation of the anterior horns of the lateral ventricles. MRI commonly shows T2-weighted signal increase in the caudate and putamen. Acanthocytes are present in 5%-50% of the red cell population. In some cases, acanthocytosis may be absent or may appear only late in the course of the disease. Increased serum concentration of muscle creatine kinase (CK) is observed in the majority of affected individuals. Muscle biopsy reveals central nuclei and atrophic fibers. VPS13A, which encodes chorein, is the only gene in which mutation is currently known to cause ChAc.
    Genetic Counseling
    ChAc is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk relatives is possible if the disease-causing mutations in the family are known. Prenatal testing is possible for families in which the disease-causing mutations are known.
    References
    Products Interactant Other Gene Complex Source Pubs Description
    BioGRID:116835 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 

    Markers

    Homology

    Clone Names

    • FLJ42030, KIAA0986

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    Golgi to endosome transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell death IEA
    Inferred from Electronic Annotation
    more info
     
    locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    protein localization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    social behavior IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    intracellular NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Preferred Names
    vacuolar protein sorting-associated protein 13A
    Names
    vacuolar protein sorting-associated protein 13A
    vacuolar protein sorting 13A
    chorea-acanthocytosis protein

    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_008931.1 RefSeqGene

      Range
      5001..245039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001018037.1NP_001018047.1  vacuolar protein sorting-associated protein 13A isoform C

      Status: REVIEWED

      Description
      Transcript Variant: This variant (C), also known as 2A, lacks an alternate in-frame segment, compared to variant A, resulting in a shorter protein (isoform C), compared to isoform A.
      Source sequence(s)
      AJ608769, AK027023, AW303378
      Consensus CDS
      CCDS55321.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000365823, OTTHUMP00000240059, ENST00000376636, OTTHUMT00000402199
      Conserved Domains (3) summary
      COG5043
      Location:42065
      Blast Score: 748
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:21692417
      Blast Score: 594
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:3119
      Blast Score: 389
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    2. NM_001018038.2NP_001018048.1  vacuolar protein sorting-associated protein 13A isoform D

      Status: REVIEWED

      Description
      Transcript Variant: This variant (D), also known as 1D, contains a distinct 3' coding region and 3' UTR, compared to variant A. The resulting isoform (D) has a shorter C-terminus compared to isoform A.
      Source sequence(s)
      AJ626859, AK027023, AW303378, BF801459, BQ011213, CB104862, CN348731
      Consensus CDS
      CCDS47983.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000365821, OTTHUMP00000240008, ENST00000376634, OTTHUMT00000052749
      Conserved Domains (3) summary
      COG5043
      Location:42104
      Blast Score: 762
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22082456
      Blast Score: 593
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:3119
      Blast Score: 388
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    3. NM_015186.3NP_056001.1  vacuolar protein sorting-associated protein 13A isoform B

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) contains a distinct 3' coding region and 3' UTR, compared to variant A. The resulting isoform (B) has a shorter C-terminus compared to isoform A.
      Source sequence(s)
      AB054005, AK027023, AW303378, BI828209, EB387114
      Consensus CDS
      CCDS6656.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000349985, OTTHUMP00000021514, ENST00000357409, OTTHUMT00000052754
      Conserved Domains (3) summary
      COG5043
      Location:42104
      Blast Score: 762
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22082456
      Blast Score: 593
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:3119
      Blast Score: 388
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    4. NM_033305.2NP_150648.2  vacuolar protein sorting-associated protein 13A isoform A

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) encodes the longest isoform (A).
      Source sequence(s)
      AB054005, AF337532, AK027023, AW303378
      Consensus CDS
      CCDS6655.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Conserved Domains (3) summary
      COG5043
      Location:42104
      Blast Score: 764
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22082456
      Blast Score: 593
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:3119
      Blast Score: 388
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000009.11 Reference GRCh37.p10 Primary Assembly

      Range
      79792361..80032399
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000141.1 Alternate HuRef

      Range
      49623817..49863840
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018920.1 Alternate CHM1_1.0

      Range
      79674022..79914074
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

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