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Aliases for VPS13D Gene

Aliases for VPS13D Gene

  • Vacuolar Protein Sorting 13 Homolog D 2 3 5
  • Vacuolar Protein Sorting 13 Homolog D (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 13D (Yeast) 2
  • KIAA0453 4

External Ids for VPS13D Gene

Previous GeneCards Identifiers for VPS13D Gene

  • GC01P012096
  • GC01P012003
  • GC01P012224
  • GC01P011443
  • GC01P012290

Summaries for VPS13D Gene

Entrez Gene Summary for VPS13D Gene

  • This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS13D Gene

VPS13D (Vacuolar Protein Sorting 13 Homolog D) is a Protein Coding gene. Diseases associated with VPS13D include Choreoacanthocytosis. An important paralog of this gene is VPS13C.

Gene Wiki entry for VPS13D Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS13D Gene

Genomics for VPS13D Gene

Regulatory Elements for VPS13D Gene

Enhancers for VPS13D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F012166 1.6 FANTOM5 Ensembl ENCODE 14.7 -52.8 -52820 21.2 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A YY1 ZNF143 ZNF207 FOS MTHFR TNFRSF1B UBIAD1 TNFRSF8 CLCN6 VPS13D DHRS3 AGTRAP MIIP MFN2
GH01F012121 0.6 Ensembl ENCODE 11.8 -108.2 -108223 1.1 ZFHX2 POLR2A BHLHE40 FOS ZNF24 EGR2 VPS13D RNU6-777P RPL23AP89 MIR7846 TNFRSF1B
GH01F012118 0.6 ENCODE 11.8 -111.3 -111271 0.2 HDGF TBL1XR1 KLF17 NFXL1 ZNF2 RAD21 SCRT2 ZNF143 ZNF207 ZNF391 VPS13D RPL23AP89 RNU6-777P UBIAD1 MIR7846 TNFRSF1B
GH01F012188 0.2 ENCODE 11.6 -41.8 -41781 0.2 BCOR SMARCA5 CTCF ZMYM3 KDM1A TNFRSF1B MIR7846 VPS13D MIR4632
GH01F012196 0.8 Ensembl ENCODE 11.5 -33.3 -33273 0.9 HDGF CTCF MAX ZNF384 RAD21 FOSL1 POLR2A SMARCA4 ADNP MYC VPS13D MIR4632 GC01P012204
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around VPS13D on UCSC Golden Path with GeneCards custom track

Promoters for VPS13D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000530773 461 1801 ATF1 CREB3L1 ARID4B SIN3A ZNF48 YY1 ZNF121 GLIS2 ELK1 ZNF207

Genomic Location for VPS13D Gene

Chromosome:
1
Start:
12,230,039 bp from pter
End:
12,512,047 bp from pter
Size:
282,009 bases
Orientation:
Plus strand

Genomic View for VPS13D Gene

Genes around VPS13D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS13D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS13D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS13D Gene

Proteins for VPS13D Gene

  • Protein details for VPS13D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5THJ4-VP13D_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 13D
    Protein Accession:
    Q5THJ4
    Secondary Accessions:
    • J3KP14
    • Q58F10
    • Q6MZK9
    • Q6ZV12
    • Q709C4
    • Q709C5
    • Q86UB4
    • Q9NSJ3
    • Q9UIM0

    Protein attributes for VPS13D Gene

    Size:
    4388 amino acids
    Molecular mass:
    491916 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC86054.1; Type=Frameshift; Positions=3074; Evidence={ECO:0000305}; Sequence=CAE46021.1; Type=Frameshift; Positions=3689; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS13D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS13D Gene

Post-translational modifications for VPS13D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS13D Gene

No data available for DME Specific Peptides for VPS13D Gene

Domains & Families for VPS13D Gene

Suggested Antigen Peptide Sequences for VPS13D Gene

Graphical View of Domain Structure for InterPro Entry

Q5THJ4

UniProtKB/Swiss-Prot:

VP13D_HUMAN :
  • Contains 1 UBA domain.
  • Belongs to the VPS13 family.
Domain:
  • Contains 1 UBA domain.
Family:
  • Belongs to the VPS13 family.
genes like me logo Genes that share domains with VPS13D: view

No data available for Gene Families for VPS13D Gene

Function for VPS13D Gene

genes like me logo Genes that share phenotypes with VPS13D: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS13D Gene

Localization for VPS13D Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS13D Gene COMPARTMENTS Subcellular localization image for VPS13D gene
Compartment Confidence
extracellular 5
cytosol 2
plasma membrane 2
endoplasmic reticulum 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IBA --
GO:0019898 extrinsic component of membrane IBA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with VPS13D: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for VPS13D Gene

Pathways & Interactions for VPS13D Gene

SuperPathways for VPS13D Gene

No Data Available

Interacting Proteins for VPS13D Gene

Selected Interacting proteins: Q5THJ4-VP13D_HUMAN for VPS13D Gene via IID

Gene Ontology (GO) - Biological Process for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA --
GO:0045053 protein retention in Golgi apparatus IBA --
genes like me logo Genes that share ontologies with VPS13D: view

No data available for Pathways by source and SIGNOR curated interactions for VPS13D Gene

Transcripts for VPS13D Gene

Unigene Clusters for VPS13D Gene

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

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS13D Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 24a · 24b ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38a · 38b ^ 39 ^ 40 ^ 41a · 41b ^ 42 ^ 43 ^ 44 ^ 45 ^
SP1: - -
SP2: - - -
SP3: - -
SP4: - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 46 ^ 47 ^ 48 ^ 49 ^ 50 ^ 51 ^ 52 ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60 ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67 ^ 68 ^ 69 ^ 70 ^ 71a ·
SP1: - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: -
SP5:
SP6: - - -
SP7:
SP8:
SP9: - -
SP10: -
SP11:
SP12:

ExUns: 71b ^ 72a · 72b · 72c · 72d · 72e ^
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for VPS13D Gene

GeneLoc Exon Structure for
VPS13D
ECgene alternative splicing isoforms for
VPS13D

Expression for VPS13D Gene

mRNA expression in normal human tissues for VPS13D Gene

Protein differential expression in normal tissues from HIPED for VPS13D Gene

This gene is overexpressed in Cerebrospinal fluid (32.4) and Esophagus (23.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS13D Gene



NURSA nuclear receptor signaling pathways regulating expression of VPS13D Gene:

VPS13D

SOURCE GeneReport for Unigene cluster for VPS13D Gene:

Hs.439381

mRNA Expression by UniProt/SwissProt for VPS13D Gene:

Q5THJ4-VP13D_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with VPS13D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for VPS13D Gene

Orthologs for VPS13D Gene

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

Orthologs for VPS13D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS13D 34 35
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia VPS13D 34 35
  • 90.43 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS13D 35
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS13D 34 35
  • 89.77 (n)
mouse
(Mus musculus)
Mammalia Vps13d 34 16 35
  • 87.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS13D 35
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps13d 34
  • 86.89 (n)
chicken
(Gallus gallus)
Aves VPS13D 34 35
  • 75.67 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 86 (a)
OneToMany
-- 35
  • 85 (a)
OneToMany
-- 35
  • 70 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13d 34
  • 70.2 (n)
zebrafish
(Danio rerio)
Actinopterygii vps13d 34 35
  • 65.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32113 34 35
  • 45.44 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009780 34
  • 27.49 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C25H3.8 34
  • 42.67 (n)
C25H3.11 35
  • 25 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 35
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 32 (a)
OneToOne
Species where no ortholog for VPS13D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • bread mold (Neurospora crassa)
  • 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 VPS13D Gene

ENSEMBL:
Gene Tree for VPS13D (if available)
TreeFam:
Gene Tree for VPS13D (if available)

Paralogs for VPS13D Gene

Paralogs for VPS13D Gene

genes like me logo Genes that share paralogs with VPS13D: view

Variants for VPS13D Gene

Sequence variations from dbSNP and Humsavar for VPS13D Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs10218648 -- 12,450,015(+) tgcta(C/T)gggag intron-variant
rs1040686 -- 12,385,567(+) GAATC(A/G)GCATG intron-variant
rs1040687 -- 12,385,569(+) ATCAG(A/C)ATGTA intron-variant
rs10442702 -- 12,281,780(+) aatta(A/G)gggtt intron-variant
rs10442703 -- 12,400,886(+) GAGTT(C/T)GAGGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS13D Gene

Variant ID Type Subtype PubMed ID
esv2667673 CNV deletion 23128226
esv2743809 CNV deletion 23290073
esv275384 CNV loss 21479260
esv3585233 CNV loss 21293372
nsv1122298 CNV deletion 24896259
nsv1124560 CNV duplication 24896259
nsv2743 CNV deletion 18451855
nsv2854 CNV deletion 18451855
nsv471622 CNV gain+loss 15918152
nsv508891 CNV insertion 20534489
nsv517848 CNV gain 19592680
nsv528439 CNV loss 19592680
nsv817617 CNV loss 17921354

Variation tolerance for VPS13D Gene

Residual Variation Intolerance Score: 0.0843% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.63; 89.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS13D Gene

Human Gene Mutation Database (HGMD)
VPS13D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS13D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS13D Gene

Disorders for VPS13D Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS13D Gene - From: DISEASES

Disorder Aliases PubMed IDs
choreoacanthocytosis
  • neuroacanthocytosis
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for VPS13D

Genetic Association Database (GAD)
VPS13D
Human Genome Epidemiology (HuGE) Navigator
VPS13D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS13D
genes like me logo Genes that share disorders with VPS13D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS13D Gene

Publications for VPS13D Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Identification of evidence suggestive of an association with peripheral arterial disease at the OSBPL10 locus by genome-wide investigation in the Japanese population. (PMID: 20610895) Koriyama H. … Morishita R. (J. Atheroscler. Thromb. 2010) 3 46 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for VPS13D Gene

Sources for VPS13D Gene

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