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

Gene ID: 23230, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:1908
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; BLTP5A; 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
mouse all
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Genomic context

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See VPS13A in Genome Data Viewer
Location:
9q21.2
Exon count:
74
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (77177534..77421537)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (89334100..89578104)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79792450..80036453)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376096 Neighboring gene MPRA-validated peak7269 silencer Neighboring gene ATP synthase membrane subunit f pseudogene 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:79694935-79696134 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:79702393-79702975 Neighboring gene replication factor C 5 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:79743283-79743791 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:79743792-79744300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:79744301-79744809 Neighboring gene Sharpr-MPRA regulatory region 10899 Neighboring gene Sharpr-MPRA regulatory region 12012 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:79793446-79793615 Neighboring gene VPS13A antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:79882068-79883068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:79883069-79884068 Neighboring gene Sharpr-MPRA regulatory region 5552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28483 Neighboring gene uncharacterized LOC124902185 Neighboring gene GNA14 antisense RNA 1 Neighboring gene G protein subunit alpha 14 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:80149170-80149682 Neighboring gene MPRA-validated peak7272 silencer Neighboring gene nuclear transport factor 2 pseudogene 3

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 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. Chorein addiction in VPS13A overexpressing rhabdomyosarcoma cells. Honisch S, et al. Oncotarget, 2015 Apr 30. PMID 25871399, Free PMC Article
  2. Choreoacanthocytosis in a Mexican family. Ruiz-Sandoval JL, et al. Arch Neurol, 2007 Nov. PMID 17998451
  3. Clinical and molecular genetic assessment of a chorea-acanthocytosis pedigree. Ichiba M, et al. J Neurol Sci, 2007 Dec 15. PMID 17673232
  4. Combined Dendritic and Axonal Deterioration Are Responsible for Motoneuronopathy in Patient-Derived Neuronal Cell Models of Chorea-Acanthocytosis. Glaß H, et al. Int J Mol Sci, 2020 Mar 5. PMID 32151030, Free PMC Article
  5. Identification of a VPS13A founder mutation in French Canadian families with chorea-acanthocytosis. Dobson-Stone C, et al. Neurogenetics, 2005 Sep. PMID 15918062

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical Features and Novel Pathogenic Variants of Chinese Patients With McLeod Syndrome and Chorea-Acanthocytosis.
    Title: Clinical Features and Novel Pathogenic Variants of Chinese Patients With McLeod Syndrome and Chorea-Acanthocytosis.
  2. An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis).
    Title: An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis).
  3. Chorein sensitive microtubule organization in tumor cells.
    Title: Chorein sensitive microtubule organization in tumor cells.
  4. Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s).
    Title: Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s).
  5. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
    Title: The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
  6. Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans.
    Title: Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans.
  7. A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
    Title: A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
  8. Structural and biochemical insights into lipid transport by VPS13 proteins.
    Title: Structural and biochemical insights into lipid transport by VPS13 proteins.
  9. XK is a partner for VPS13A: a molecular link between Chorea-Acanthocytosis and McLeod Syndrome.
    Title: XK is a partner for VPS13A: a molecular link between Chorea-Acanthocytosis and McLeod Syndrome.
  10. Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances.
    Title: Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances.
Submit: New GeneRIF Correction See all GeneRIFs (39)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Chorea-acanthocytosis
MedGen: C0393576 OMIM: 200150 GeneReviews: VPS13A Disease
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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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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 adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in brain-derived neurotrophic factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to osmotic stress IEA
Inferred from Electronic Annotation
more info
  
involved_in erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in exploration behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in flagellated sperm motility IEA
Inferred from Electronic Annotation
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in lipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in long-term synaptic depression IEA
Inferred from Electronic Annotation
more info
  
involved_in lysosomal protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in microglia differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in motor behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in neuroinflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in neuromuscular process controlling balance IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron projection arborization 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
  
involved_in protein secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to environmental enrichment IEA
Inferred from Electronic Annotation
more info
  
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 
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 mitochondria-associated endoplasmic reticulum membrane contact site 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 mitochondrion HTP PubMed 
located_in neuron projection IEA
Inferred from Electronic Annotation
more info
  
located_in neuronal cell body IEA
Inferred from Electronic Annotation
more info
  
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

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Preferred Names
intermembrane lipid transfer protein VPS13A
Names
bridge-like lipid transfer protein family member 5A
chorea-acanthocytosis protein
vacuolar protein sorting 13A
vacuolar protein sorting-associated protein 13A

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_008931.2 RefSeqGene

    Range
    5002..249005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001018037.2 → NP_001018047.1  intermembrane lipid transfer protein VPS13A 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
    Related
    ENSP00000365823.3, ENST00000376636.7
    Conserved Domains (7) summary
    COG5043
    Location:4 → 2065
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2170 → 2413
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:2907 → 2986
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2727 → 2904
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 793
    VPS13_mid_rpt; Repeating coiled region of VPS13

  2. NM_001018038.3 → NP_001018048.1  intermembrane lipid transfer protein VPS13A 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
    Related
    ENSP00000496361.1, ENST00000645632.1
    Conserved Domains (7) summary
    COG5043
    Location:4 → 2104
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2209 → 2452
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:2946 → 3025
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2766 → 2943
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 793
    VPS13_mid_rpt; Repeating coiled region of VPS13

  3. NM_015186.4 → NP_056001.1  intermembrane lipid transfer protein VPS13A 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
    Related
    ENSP00000493592.1, ENST00000643348.1
    Conserved Domains (7) summary
    COG5043
    Location:4 → 2104
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2209 → 2452
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:2946 → 3025
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2766 → 2943
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 793
    VPS13_mid_rpt; Repeating coiled region of VPS13

  4. NM_033305.3 → NP_150648.2  intermembrane lipid transfer protein VPS13A 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
    Q5JSX9, Q5JSY0, Q5VYR5, Q702P4, Q709D0, Q86YF8, Q96RL7, Q96S61, Q9H995, Q9Y2J1
    Related
    ENSP00000353422.3, ENST00000360280.8
    Conserved Domains (7) summary
    COG5043
    Location:4 → 2104
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2209 → 2452
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:2946 → 3025
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 371
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:2766 → 2943
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 793
    VPS13_mid_rpt; Repeating coiled region of VPS13

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    89334100..89578104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96RL7.2 GenPept UniProtKB/Swiss-Prot:Q96RL7

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