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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

Additional gene information for VPS13D Gene

No data available for CIViC summary , 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
GH01H012166 1.8 FANTOM5 ENCODE dbSUPER 14.4 -55.6 -55624 15 HDGF FOXA2 PKNOX1 ARNT YY1 ZNF766 ZNF143 ZNF207 FOS REST MTHFR TNFRSF1B TNFRSF8 CLCN6 VPS13D AGTRAP MIIP MFN2 MIR4632
GH01H011907 1.8 FANTOM5 ENCODE dbSUPER 12.6 -321.2 -321242 3 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A PPARGC1A TARDBP UBIAD1 ENSG00000226849 EXOSC10 SNORA59A ENSG00000271895 CLCN6 RNU5E-1 RNU5E-4P LOC102724659
GH01H012182 1.7 FANTOM5 Ensembl ENCODE dbSUPER 12.7 -44.9 -44927 5 PTBP1 RAD21 GATA2 ZNF366 FOS RCOR1 RUNX3 IKZF2 SMARCA5 ZC3H11A TNFRSF1B VPS13D TNFRSF8 AGTRAP MTHFR CLCN6 MIR4632
GH01H012614 1.7 FANTOM5 ENCODE dbSUPER 11.8 +387.4 387350 6 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 VPS13D DHRS3 MIR6730
GH01H012014 1.4 Ensembl ENCODE dbSUPER 12.5 -215.3 -215272 1 HDAC1 TBP ZBTB40 EGR1 POLR3A CREM SMARCA5 ZBTB11 REST ELF1 MFN2 EXOSC10 MTOR VPS13D ENSG00000226849 ENSG00000271895 MIIP KIAA2013 ENSG00000270914
- Elite enhancer and/or Elite enhancer-gene association 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
ENSR00000001521 461 1801 HDGF ATF1 ARNT ARID4B SIN3A YY1 GLIS2 ELK1 ZNF207 ZNF143

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

Gene Families for VPS13D Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for VPS13D Gene

Graphical View of Domain Structure for InterPro Entry

Q5THJ4

UniProtKB/Swiss-Prot:

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

Function for VPS13D Gene

Phenotypes From GWAS Catalog for VPS13D Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VPS13D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
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 VPS13D gene
Compartment Confidence
extracellular 5
plasma membrane 2
cytosol 2
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
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

None

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

Drugs & Compounds for VPS13D Gene

No Compound Related Data Available

Transcripts for VPS13D Gene

Unigene Clusters for VPS13D Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VPS13D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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.

Evidence on tissue expression from TISSUES for VPS13D Gene

  • Liver(4.2)
  • Nervous system(4.2)
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 , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia VPS13D 33 34
  • 90.43 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS13D 34
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS13D 33 34
  • 89.77 (n)
mouse
(Mus musculus)
Mammalia Vps13d 33 16 34
  • 87.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS13D 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps13d 33
  • 86.89 (n)
chicken
(Gallus gallus)
Aves VPS13D 33 34
  • 75.67 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 86 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 70 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13d 33
  • 70.2 (n)
zebrafish
(Danio rerio)
Actinopterygii vps13d 33 34
  • 65.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32113 33 34
  • 45.44 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009780 33
  • 27.49 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C25H3.8 33
  • 42.67 (n)
C25H3.11 34
  • 25 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 34
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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
rs1000004030 -- 12,399,826(+) AAAAC(-/A)AAAAA intron-variant
rs1000008972 -- 12,437,949(+) GGCAA(A/T)TGTGG intron-variant
rs1000016302 -- 12,393,311(+) CAAAC(C/G)TGGAG intron-variant
rs1000018274 -- 12,354,427(+) TTCTC(A/G)GGAGG intron-variant
rs1000020165 -- 12,258,358(+) CCCAC(A/C)CCCCT 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: HGMD and 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 JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  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 (Journal of atherosclerosis and thrombosis 2010) 3 45 60
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for VPS13D Gene

Sources for VPS13D Gene

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