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

    Gene ID: 23230, updated on 22-Apr-2017
    Official Symbol
    VPS13Aprovided by HGNC
    Official Full Name
    vacuolar protein sorting 13 homolog Aprovided by HGNC
    Primary source
    HGNC:HGNC:1908
    See related
    Ensembl:ENSG00000197969 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]
    Orthologs
    Location:
    9q21.2
    Exon count:
    76
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (77177353..77421537)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79792269..80032399)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376096 Neighboring gene ATP synthase, H+ transporting, mitochondrial Fo complex subunit F2 pseudogene 3 Neighboring gene replication factor C 5 pseudogene 1 Neighboring gene VPS13A antisense RNA 1 Neighboring gene GNA14 antisense RNA 1 Neighboring gene G protein subunit alpha 14 Neighboring gene nuclear transport factor 2 pseudogene 3

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    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 
    autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    dense core granule IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Preferred Names
    vacuolar protein sorting-associated protein 13A
    Names
    chorea-acanthocytosis protein
    vacuolar protein sorting 13A

    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

      See identical proteins and their annotated locations for NP_001018047.1

      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
      ENSP00000365823.3, OTTHUMP00000240059, ENST00000376636.7, OTTHUMT00000402199
      Conserved Domains (7) summary
      COG5043
      Location:42065
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:21702413
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:29072986
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:4113
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:142371
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:27272904
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:570793
      VPS13_mid_rpt; Repeating coiled region of VPS13
    2. NM_001018038.2NP_001018048.1  vacuolar protein sorting-associated protein 13A isoform D

      See identical proteins and their annotated locations for NP_001018048.1

      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
      ENSP00000365821.4, OTTHUMP00000240008, ENST00000376634.8, OTTHUMT00000052749
      Conserved Domains (7) summary
      COG5043
      Location:42104
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22092452
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:29463025
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:4113
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:142371
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:27662943
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:570793
      VPS13_mid_rpt; Repeating coiled region of VPS13
    3. NM_015186.3NP_056001.1  vacuolar protein sorting-associated protein 13A isoform B

      See identical proteins and their annotated locations for NP_056001.1

      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
      ENSP00000349985.5, OTTHUMP00000021514, ENST00000357409.9, OTTHUMT00000052754
      Conserved Domains (7) summary
      COG5043
      Location:42104
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22092452
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:29463025
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:4113
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:142371
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:27662943
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:570793
      VPS13_mid_rpt; Repeating coiled region of VPS13
    4. NM_033305.2NP_150648.2  vacuolar protein sorting-associated protein 13A isoform A

      See identical proteins and their annotated locations for NP_150648.2

      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
      Related
      ENSP00000353422.3, OTTHUMP00000021513, ENST00000360280.7, OTTHUMT00000052753
      Conserved Domains (7) summary
      COG5043
      Location:42104
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      pfam06650
      Location:22092452
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:29463025
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:4113
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:142371
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:27662943
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:570793
      VPS13_mid_rpt; Repeating coiled region of VPS13

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      77177353..77421537
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001746260.1 RNA Sequence

    2. XR_001746259.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      79938844..80179199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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