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... See more...

Aliases for VPS13D Gene

Aliases for VPS13D Gene

  • Vacuolar Protein Sorting 13 Homolog D 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 13D 3 4
  • Vacuolar Protein Sorting 13 Homolog D (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 13D (Yeast) 2
  • Vacuolar Protein Sorting 13D 3
  • KIAA0453 4
  • SCAR4 3

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 Spinocerebellar Ataxia, Autosomal Recessive 4 and Vps13d Movement Disorder. An important paralog of this gene is VPS13C.

UniProtKB/Swiss-Prot Summary for VPS13D Gene

  • Functions in promoting mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission (PubMed:29307555, PubMed:29604224). Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis.

Gene Wiki entry for VPS13D Gene

Additional gene information for VPS13D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification 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 EPDnew Ensembl ENCODE CraniofacialAtlas 750.6 +1.0 968 4 ZNF24 SP1 CTCF SIX5 POLR2A HCFC1 RUNX1 L3MBTL2 DACH1 NKRF VPS13D UBIAD1 AGTRAP SNORA59A RF00994-002
GH01J012228 Enhancer 0.3 Ensembl 750.6 -1.6 -1629 0.4 SP7 VPS13D ENSG00000252969
GH01J012166 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 14.7 -53.0 -53019 21.6 ZNF24 ZBTB40 FOXA1 SMARCE1 POLR2A RUNX1 MYC CC2D1A ELF1 L3MBTL2 TNFRSF1B MTHFR AGTRAP TNFRSF8 CLCN6 VPS13D SNORA59A KIAA2013 MIIP MFN2
GH01J012014 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.5 -215.6 -215585 2 ZBTB40 SMARCE1 ELF1 L3MBTL2 DACH1 TEAD4 ZFX MLLT1 CBFA2T2 PRDM1 MFN2 EXOSC10 MTOR VPS13D ENSG00000226849 ENSG00000271895 MIIP KIAA2013 ENSG00000270914 piR-50308-007
GH01J011943 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.7 -285.6 -285631 2.1 CTBP1 ZNF362 ZNF701 ZNF280D ZNF473 SP7 ZSCAN21 ZNF548 PRDM1 GLIS2 EXOSC10 TARDBP ENSG00000226849 CLCN6 MTHFR MFN2 RNU5E-4P RNU5E-1 C1orf167-AS1 PRAMEF30P
- 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:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • Bach1
  • Chx10
  • MyoD
  • POU3F1
  • PPAR-gamma1
  • PPAR-gamma2
  • RSRFC4

Genomic Locations for VPS13D Gene

Genomic Locations for VPS13D Gene
chr1:12,230,030-12,512,047
(GRCh38/hg38)
Size:
282,018 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

Suggested Antigen Peptide Sequences for VPS13D Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar protein sorting 13 homolog D (S. cerevisiae) (B1AJZ2_HUMAN)
  • Vacuolar protein sorting-associated protein 13D (VP13D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5THJ4

UniProtKB/Swiss-Prot:

VP13D_HUMAN :
  • The UBA domain is required for mitochondrial size regulation.
  • Belongs to the VPS13 family.
Domain:
  • The UBA domain is required for mitochondrial size regulation.
Family:
  • Belongs to the VPS13 family.
genes like me logo Genes that share domains with VPS13D: view

Function for VPS13D Gene

Molecular function for VPS13D Gene

UniProtKB/Swiss-Prot Function:
Functions in promoting mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission (PubMed:29307555, PubMed:29604224). Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis.

Phenotypes From GWAS Catalog for VPS13D Gene

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

Human Phenotype Ontology for VPS13D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
plasma membrane 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1
peroxisome 0

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:0005623 cell IEA --
GO:0019898 extrinsic component of membrane IBA 21873635
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

PathCards logo

SuperPathways for VPS13D Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS13D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA 21873635
GO:0007005 mitochondrion organization IBA,IMP 29307555
GO:0045053 protein retention in Golgi apparatus IBA 21873635
GO:1901526 positive regulation of mitophagy IMP 29307555
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

CRISPR Products

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 33 32
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS13D 33 32
  • 90.43 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS13D 33
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS13D 33 32
  • 89.77 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps13d 17 33 32
  • 87.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS13D 33
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps13d 32
  • 86.89 (n)
chicken
(Gallus gallus)
Aves VPS13D 33 32
  • 75.67 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 86 (a)
OneToMany
-- 33
  • 85 (a)
OneToMany
-- 33
  • 70 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13d 32
  • 70.2 (n)
zebrafish
(Danio rerio)
Actinopterygii vps13d 33 32
  • 65.36 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG32113 33 32
  • 45.44 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009780 32
  • 27.49 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C25H3.8 32
  • 42.67 (n)
C25H3.11 33
  • 25 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 33
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 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
rs1191625571 Spinocerebellar ataxia, autosomal recessive 4 (SCAR4) [MIM:607317] 12,355,977(+) G/A coding_sequence_variant, missense_variant
rs1383958401 Spinocerebellar ataxia, autosomal recessive 4 (SCAR4) [MIM:607317] 12,276,181(+) A/G coding_sequence_variant, missense_variant
rs1557478316 pathogenic, Spinocerebellar ataxia autosomal recessive 4 12,497,520(+) G/A coding_sequence_variant, missense_variant
rs1557680710 pathogenic, Spinocerebellar ataxia autosomal recessive 4 12,276,904(+) C/T coding_sequence_variant, stop_gained
rs1557680919 pathogenic, Spinocerebellar ataxia autosomal recessive 4 12,277,157(+) G/A coding_sequence_variant, missense_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

(3) MalaCards diseases for VPS13D Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

VP13D_HUMAN
  • Spinocerebellar ataxia, autosomal recessive 4 (SCAR4) [MIM:607317]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR4 patients manifest ataxic gait with spasticity and hyperreflexia of the lower limbs resulting in difficulty walking. The age at onset is highly variable, ranging from early childhood to adulthood. {ECO:0000269 PubMed:29518281, ECO:0000269 PubMed:29604224}. Note=The disease is caused by mutations affecting the gene represented in this entry.

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 Genatlas for VPS13D Gene

Publications for VPS13D Gene

  1. Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the Regulation of Mitochondrial Size and Clearance. (PMID: 29307555) Anding AL … Baehrecke EH (Current biology : CB 2018) 3 4 56
  2. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. (PMID: 29604224) Seong E … Burmeister M (Annals of neurology 2018) 3 4 56
  3. Recessive mutations in >VPS13D cause childhood onset movement disorders. (PMID: 29518281) Gauthier J … Campeau PM (Annals of neurology 2018) 3 4 56
  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 43 56
  5. 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 43 56

Products for VPS13D Gene

Sources for VPS13D Gene