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Aliases for VPS13A Gene

Aliases for VPS13A Gene

  • Vacuolar Protein Sorting 13 Homolog A 2 3 5
  • Chorein 2 3 4
  • Chorea-Acanthocytosis Protein 3 4
  • CHAC 3 4
  • Vacuolar Protein Sorting 13 Homolog A (S. Cerevisiae) 2
  • Vacuolar Protein Sorting-Associated Protein 13A 3
  • Vacuolar Protein Sorting 13A (Yeast) 2
  • Vacuolar Protein Sorting 13A 3
  • Chorea Acanthocytosis 2
  • KIAA0986 4

External Ids for VPS13A Gene

Previous HGNC Symbols for VPS13A Gene

  • CHAC

Previous GeneCards Identifiers for VPS13A Gene

  • GC09P075249
  • GC09P077021
  • GC09P078982
  • GC09P079793
  • GC09P049623

Summaries for VPS13A Gene

Entrez Gene Summary for VPS13A Gene

  • 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]

GeneCards Summary for VPS13A Gene

VPS13A (Vacuolar Protein Sorting 13 Homolog A) is a Protein Coding gene. Diseases associated with VPS13A include Choreoacanthocytosis and Curly Hair-Acral Keratoderma-Caries Syndrome. An important paralog of this gene is VPS13C.

UniProtKB/Swiss-Prot for VPS13A Gene

  • May play a role in the control of protein cycling through the trans-Golgi network to early and late endosomes, lysosomes and plasma membrane.

Gene Wiki entry for VPS13A Gene

Additional gene information for VPS13A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS13A Gene

Genomics for VPS13A Gene

GeneHancer (GH) Regulatory Elements for VPS13A Gene

Promoters and enhancers for VPS13A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I077176 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 598.9 +0.6 574 3.4 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 VPS13A PIR35220 VPS13A-AS1
GH09I077158 Enhancer 0.5 ENCODE 33 -18.3 -18334 2 MAFF JUN CEBPB EP300 MAFK VPS13A PIR35220 RFC5P1
GH09I077417 Enhancer 0.6 Ensembl ENCODE 19.8 +240.6 240577 1.5 PRDM6 CEBPB GC09P077420 VPS13A GC09M077235
GH09I077167 Enhancer 0.6 ENCODE 18.8 -9.8 -9793 0.2 CTCF ZNF654 TRIM22 ZNF384 RAD21 MAFF SMC3 ZNF143 VPS13A PIR35220 RFC5P1
GH09I076905 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 4.9 -271.1 -271070 1.3 CLOCK INSM2 KLF17 ZNF76 SIN3A FEZF1 RFX5 ZNF335 GLIS2 ELK1 PRUNE2 VPS13A GC09M076829
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VPS13A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS13A gene promoter:

Genomic Locations for VPS13A Gene

Genomic Locations for VPS13A Gene
244,189 bases
Plus strand

Genomic View for VPS13A Gene

Genes around VPS13A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS13A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS13A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS13A Gene

Proteins for VPS13A Gene

  • Protein details for VPS13A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Vacuolar protein sorting-associated protein 13A
    Protein Accession:
    Secondary Accessions:
    • Q5JSX9
    • Q5JSY0
    • Q5VYR5
    • Q702P4
    • Q709D0
    • Q86YF8
    • Q96S61
    • Q9H995
    • Q9Y2J1

    Protein attributes for VPS13A Gene

    3174 amino acids
    Molecular mass:
    360276 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH20576.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS13A Gene


neXtProt entry for VPS13A Gene

Post-translational modifications for VPS13A Gene

  • Ubiquitination at isoforms=2, 3, 42228, posLast=29232923, posLast=29882988, and isoforms=2, 3, 43000
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS13A Gene

Domains & Families for VPS13A Gene

Gene Families for VPS13A Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for VPS13A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the VPS13 family.
  • Belongs to the VPS13 family.
genes like me logo Genes that share domains with VPS13A: view

Function for VPS13A Gene

Molecular function for VPS13A Gene

UniProtKB/Swiss-Prot Function:
May play a role in the control of protein cycling through the trans-Golgi network to early and late endosomes, lysosomes and plasma membrane.

Phenotypes From GWAS Catalog for VPS13A Gene

Gene Ontology (GO) - Molecular Function for VPS13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17474147
genes like me logo Genes that share ontologies with VPS13A: view
genes like me logo Genes that share phenotypes with VPS13A: view

Human Phenotype Ontology for VPS13A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VPS13A Gene

MGI Knock Outs for VPS13A:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VPS13A Gene

Localization for VPS13A Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS13A gene
Compartment Confidence
mitochondrion 3
cytosol 3
plasma membrane 2
cytoskeleton 1
endoplasmic reticulum 1
endosome 1

Gene Ontology (GO) - Cellular Components for VPS13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular NAS 11381254
GO:0005829 cytosol IEA --
GO:0031045 dense core granule IEA --
genes like me logo Genes that share ontologies with VPS13A: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for VPS13A Gene

Pathways & Interactions for VPS13A Gene

SuperPathways for VPS13A Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006895 Golgi to endosome transport NAS 11381253
GO:0006914 autophagy IMP 25996471
GO:0007399 nervous system development IEA --
GO:0007626 locomotory behavior IEA --
genes like me logo Genes that share ontologies with VPS13A: view

No data available for Pathways by source and SIGNOR curated interactions for VPS13A Gene

Drugs & Compounds for VPS13A Gene

(1) Drugs for VPS13A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with VPS13A: view

Transcripts for VPS13A Gene

Unigene Clusters for VPS13A Gene

Vacuolar protein sorting 13 homolog A (S. cerevisiae):
Representative Sequences:

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS13A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a ·
SP1: -

ExUns: 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33 ^ 34
SP9: -

Relevant External Links for VPS13A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VPS13A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS13A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VPS13A Gene

This gene is overexpressed in Ovary (28.5), Peripheral blood mononuclear cells (9.3), Blymphocyte (6.8), and Heart (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VPS13A Gene

Protein tissue co-expression partners for VPS13A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS13A Gene:


SOURCE GeneReport for Unigene cluster for VPS13A Gene:


mRNA Expression by UniProt/SwissProt for VPS13A Gene:

Tissue specificity: Widely expressed. Higher expression is found in brain, heart, skeletal muscle and kidney.

Evidence on tissue expression from TISSUES for VPS13A Gene

  • Nervous system(4.6)
  • Blood(4.5)
  • Liver(4.3)
  • Muscle(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS13A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • face
  • head
  • lip
  • mouth
  • pharynx
  • salivary gland
  • tongue
  • esophagus
  • kidney
  • stomach
  • foot
  • lower limb
  • upper limb
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with VPS13A: view

No data available for mRNA differential expression in normal tissues for VPS13A Gene

Orthologs for VPS13A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VPS13A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia VPS13A 33 34
  • 99.76 (n)
(Canis familiaris)
Mammalia VPS13A 33 34
  • 90.5 (n)
(Bos Taurus)
Mammalia -- 34
  • 89 (a)
VPS13A 33
  • 88.08 (n)
-- 34
  • 85 (a)
(Rattus norvegicus)
Mammalia Vps13a 33
  • 85.52 (n)
(Mus musculus)
Mammalia Vps13a 33 16 34
  • 85.19 (n)
(Monodelphis domestica)
Mammalia VPS13A 34
  • 73 (a)
(Ornithorhynchus anatinus)
Mammalia VPS13A 34
  • 66 (a)
(Gallus gallus)
Aves VPS13A 33 34
  • 70.81 (n)
(Anolis carolinensis)
Reptilia VPS13A 34
  • 62 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13a 33
  • 66.94 (n)
(Danio rerio)
Actinopterygii vps13a 33 34
  • 58.25 (n)
chac 33
fruit fly
(Drosophila melanogaster)
Insecta Vps13 33 34
  • 46.09 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005082 33
  • 45.17 (n)
(Caenorhabditis elegans)
Secernentea T08G11.1 33 34
  • 46.85 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 33 34 36
  • 43.8 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL064C 33
  • 43.04 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E00705g 33
  • 42.36 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05837 33
  • 42.08 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6732 33
Species where no ortholog for VPS13A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS13A Gene

Gene Tree for VPS13A (if available)
Gene Tree for VPS13A (if available)

Paralogs for VPS13A Gene

Paralogs for VPS13A Gene

(1) SIMAP similar genes for VPS13A Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VPS13A: view

Variants for VPS13A Gene

Sequence variations from dbSNP and Humsavar for VPS13A Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1034458059 uncertain-significance, Choreoacanthocytosis 77,321,711(+) C/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1042881230 uncertain-significance, Choreoacanthocytosis 77,227,429(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1048743 likely-benign, Choreoacanthocytosis 77,416,948(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1057515644 uncertain-significance, Choreoacanthocytosis 77,177,547(+) G/C 5_prime_UTR_variant, non_coding_transcript_variant
rs1057515645 uncertain-significance, Choreoacanthocytosis 77,201,379(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS13A Gene

Variant ID Type Subtype PubMed ID
dgv7682n100 CNV gain 25217958
esv2613215 CNV deletion 19546169
esv2672384 CNV deletion 23128226
esv3620768 CNV loss 21293372
esv3620769 CNV loss 21293372
esv3620770 CNV loss 21293372
esv3620771 CNV loss 21293372
esv3620772 CNV loss 21293372
esv3620773 CNV loss 21293372
esv7342 OTHER inversion 19470904
nsv1041647 CNV gain 25217958
nsv1051079 CNV gain 25217958
nsv521364 CNV loss 19592680
nsv614728 CNV loss 21841781
nsv614729 CNV loss 21841781

Variation tolerance for VPS13A Gene

Residual Variation Intolerance Score: 0.614% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.41; 71.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS13A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS13A Gene

Disorders for VPS13A Gene

MalaCards: The human disease database

(9) MalaCards diseases for VPS13A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Choreoacanthocytosis (CHAC) [MIM:200150]: An autosomal recessive neurodegenerative disorder characterized by the gradual onset of hyperkinetic movements and abnormal erythrocyte morphology. Basal ganglia atrophy in the brain is a pathological feature of the disease. Other clinical symptoms include psychiatric features, epilepsy, peripheral neuropathy, myopathy and oral self-mutilation. {ECO:0000269 PubMed:11381253, ECO:0000269 PubMed:12404112}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VPS13A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VPS13A: view

No data available for Genatlas for VPS13A Gene

Publications for VPS13A Gene

  1. Analysis of the human VPS13 gene family. (PMID: 15498460) Velayos-Baeza A … Monaco AP (Genomics 2004) 3 4 22 58
  2. A conserved sorting-associated protein is mutant in chorea-acanthocytosis. (PMID: 11381253) Rampoldi L … Monaco AP (Nature genetics 2001) 2 3 4 58
  3. The gene encoding a newly discovered protein, chorein, is mutated in chorea-acanthocytosis. (PMID: 11381254) Ueno S … Sano A (Nature genetics 2001) 3 4 22 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Clinical and molecular genetic assessment of a chorea-acanthocytosis pedigree. (PMID: 17673232) Ichiba M … Sano A (Journal of the neurological sciences 2007) 3 22 58

Products for VPS13A Gene

Sources for VPS13A Gene

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