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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-Associated Protein 13D 3
  • Vacuolar Protein Sorting 13D (Yeast) 2
  • Vacuolar Protein Sorting 13D 3
  • 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

GeneHancer (GH) Regulatory Elements for VPS13D Gene

Promoters and enhancers for VPS13D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J012229 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 650.7 +1.2 1178 3.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A YY1 ZNF207 ZNF143 SP3 VPS13D UBIAD1 GC01P012251 PIR35697
GH01J012166 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 14.4 -55.6 -55617 15.6 HDGF FOXA2 PKNOX1 SMAD1 ARNT IRF4 YY1 ZNF766 ZNF207 ZNF143 TNFRSF1B MTHFR TNFRSF8 CLCN6 VPS13D AGTRAP MIIP MFN2 MIR7846 MIR4632
GH01J012614 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.8 +387.4 387356 6.8 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC DHRS3 ENSG00000272482 VPS13D MIR6730
GH01J011907 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -321.2 -321235 3.1 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 RNU5E-1 RNU5E-4P TARDBP ENSG00000226849 UBIAD1 EXOSC10 SNORA59A ENSG00000271895 CLCN6 LOC102724659
GH01J012590 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 11.4 +365.1 365091 9 FOXA2 SIN3A ZNF2 BRCA1 ZNF48 YY1 ZNF143 FOS PAF1 RXRA VPS13D MIR6730 DHRS3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS13D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS13D gene promoter:
  • Bach1
  • POU3F1
  • RSRFC4
  • MyoD
  • PPAR-gamma2
  • PPAR-gamma1
  • Chx10
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta

Genomic Locations for VPS13D Gene

Genomic Locations for VPS13D Gene
chr1:12,230,032-12,512,047
(GRCh38/hg38)
Size:
282,016 bases
Orientation:
Plus strand
chr1:12,290,113-12,572,099
(GRCh37/hg19)
Size:
281,987 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

Protein Domains for VPS13D Gene

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

Clone 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
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
endosome 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:0019898 extrinsic component of membrane IBA --
GO:0070062 extracellular exosome HDA 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

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

Drugs & Compounds for VPS13D Gene

No Compound Related Data Available

Transcripts for VPS13D Gene

mRNA/cDNA for VPS13D Gene

(2) REFSEQ mRNAs :
(22) Additional mRNA sequences :
(359) Selected AceView cDNA sequences:
(20) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VPS13D Gene

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

Clone 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 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

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 34 33
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS13D 34 33
  • 90.43 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS13D 34
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS13D 34 33
  • 89.77 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps13d 16 34 33
  • 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 34 33
  • 75.67 (n)
OneToOne
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 34 33
  • 65.36 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG32113 34 33
  • 45.44 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for VPS13D: view image

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 Variation AA Info Type
rs1000004030 -- 12,399,826(+) AAAAAAA/AAAAAA intron_variant
rs1000008972 -- 12,437,949(+) A/T intron_variant
rs1000016302 -- 12,393,311(+) C/G intron_variant
rs1000018274 -- 12,354,427(+) A/G intron_variant
rs1000020165 -- 12,258,358(+) A/C 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)

Additional Variant Information 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
  • chac
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for VPS13D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 44 58
  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 44 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  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 58

Products for VPS13D Gene

Sources for VPS13D Gene

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