Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 23230, updated on 4-Jul-2021

    Summary

    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
    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]
    Expression
    Ubiquitous expression in testis (RPKM 7.5), skin (RPKM 6.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS13A in Genome Data Viewer
    Location:
    9q21.2
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (77177534..77421537)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79792450..80036453)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene replication factor C 5 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 10899 Neighboring gene Sharpr-MPRA regulatory region 12012 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

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ42030, KIAA0986

    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 Golgi to endosome transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in flagellated sperm motility IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lysosomal protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in protein retention in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in social behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sperm mitochondrion organization IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extrinsic component of membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in extrinsic component of membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lipid droplet IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial outer membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal dense core vesicle lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in sperm midpiece IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 13A
    Names
    chorea-acanthocytosis protein
    vacuolar protein sorting 13A

    NCBI Reference Sequences (RefSeq)

    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

    1. NG_008931.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001018037.2NP_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, AL158159, AW303378
      Consensus CDS
      CCDS55321.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000365823.3, ENST00000376636.7
      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_001018038.3NP_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
      ENSP00000496361.1, ENST00000645632.1
      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_015186.4NP_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, EB387114
      Consensus CDS
      CCDS6656.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000493592.1, ENST00000643348.1
      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_033305.3NP_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, AL158159, AW303378
      Consensus CDS
      CCDS6655.1
      UniProtKB/Swiss-Prot
      Q96RL7
      Related
      ENSP00000353422.3, ENST00000360280.8
      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 Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      77177534..77421537
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center