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

Gene ID: 23230, updated on 17-Jun-2019

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

Genomic context

See VPS13A in Genome Data Viewer
Location:
9q21.2
Exon count:
76
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 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 membrane subunit f 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

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 FunctionsWhat'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
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 IBA
Inferred from Biological aspect of Ancestor
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 retention in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
extrinsic component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001018038.2NP_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
    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_015186.3NP_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, ENST00000357409.9
    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 Annotation Release 109

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

RNA

  1. XR_001746260.1 RNA Sequence

  2. XR_001746259.1 RNA Sequence

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