This gene encodes a member of the vacuolar protein sorting-associated 13 gene family. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010] See more...

Aliases for VPS13C Gene

Aliases for VPS13C Gene

  • Vacuolar Protein Sorting 13 Homolog C 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 13C 3 4
  • KIAA1421 2 4
  • Vacuolar Protein Sorting 13 Homolog C (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 13C (Yeast) 2
  • FLJ20136 2
  • FLJ10381 2
  • PARK23 3
  • VPS13C 5

External Ids for VPS13C Gene

Previous GeneCards Identifiers for VPS13C Gene

  • GC15M059860
  • GC15M059931
  • GC15M062144
  • GC15M038966

Summaries for VPS13C Gene

Entrez Gene Summary for VPS13C Gene

  • This gene encodes a member of the vacuolar protein sorting-associated 13 gene family. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010]

GeneCards Summary for VPS13C Gene

VPS13C (Vacuolar Protein Sorting 13 Homolog C) is a Protein Coding gene. Diseases associated with VPS13C include Parkinson Disease 23, Autosomal Recessive Early-Onset and Parkinson Disease, Late-Onset. An important paralog of this gene is VPS13A.

UniProtKB/Swiss-Prot Summary for VPS13C Gene

  • Necessary for proper mitochondrial function and maintenance of mitochondrial transmembrane potential. Involved in the regulation of PINK1/PRKN-mediated mitophagy in response to mitochondrial depolarization.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS13C Gene

Genomics for VPS13C Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VPS13C 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
GH15J062059 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 613.7 +0.1 73 3.6 GATAD2A CTCF HNRNPL ZNF629 PRDM10 TFE3 RFX1 IKZF1 POLR2A ZNF7 VPS13C LOC101928907 C2CD4A piR-38005-012 RORA
GH15J062811 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 42.1 -751.7 -751734 2.4 GATAD2A TFE3 SOX13 RXRB IRF2 SP1 CEBPA ZNF140 ETS1 TGIF2 HQ292129 VPS13C USP3 USP3-AS1 ENSG00000259370 piR-51471 TPM1 TLN2
GH15J063037 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 -986.9 -986934 20.2 HNRNPL GATAD2A CTCF TEAD4 PRDM10 ZNF629 RFX1 LEF1 IKZF1 ZNF692 TPM1 TPM1-AS RPS27L VPS13C RAB8B LACTB NONHSAG017121.2 lnc-RPS27L-8
GH15J062035 Enhancer 0.6 Ensembl ENCODE 26.3 +24.5 24512 1.7 JUND PRDM1 JUN POLR2A VPS13C LOC101928907 piR-38352-203 piR-39858-218 RORA
GH15J061528 Enhancer 0.7 Ensembl ENCODE 13.9 +531.7 531672 2.4 CTCF FOXA2 POLR2A RCOR1 FOXA1 SMARCA4 EZH2 EGR1 ZNF548 VPS13C LOC101928850 L13714-152 ENSG00000259616 LOC107984782 RORA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS13C on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS13C

Top Transcription factor binding sites by QIAGEN in the VPS13C gene promoter:
  • AML1a
  • Egr-2
  • FOXO3
  • NF-E2
  • NF-E2 p45
  • Pax-4a
  • POU3F2
  • USF-1
  • USF1

Genomic Locations for VPS13C Gene

Genomic Locations for VPS13C Gene
chr15:61,852,389-62,060,473
(GRCh38/hg38)
Size:
208,085 bases
Orientation:
Minus strand
chr15:62,144,588-62,352,672
(GRCh37/hg19)
Size:
208,085 bases
Orientation:
Minus strand

Genomic View for VPS13C Gene

Genes around VPS13C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS13C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS13C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS13C Gene

Proteins for VPS13C Gene

  • Protein details for VPS13C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q709C8-VP13C_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 13C
    Protein Accession:
    Q709C8
    Secondary Accessions:
    • Q6ISR4
    • Q702P2
    • Q702P3
    • Q709C9
    • Q9NXN8
    • Q9P2C6

    Protein attributes for VPS13C Gene

    Size:
    3753 amino acids
    Molecular mass:
    422390 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA90972.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA92659.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS13C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS13C Gene

Post-translational modifications for VPS13C Gene

  • Ubiquitination at Lys578, Lys2155, Lys2233, Lys2304, Lys2777, Lys3487, Lys3496, Lys3501, and Lys3557
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS13C Gene

Domains & Families for VPS13C Gene

Gene Families for VPS13C Gene

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

Protein Domains for VPS13C Gene

InterPro:
Blocks:
  • Protein of unknown function DUF1162
ProtoNet:

Suggested Antigen Peptide Sequences for VPS13C Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar protein sorting-associated protein 13C (VP13C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q709C8

UniProtKB/Swiss-Prot:

VP13C_HUMAN :
  • Belongs to the VPS13 family.
Family:
  • Belongs to the VPS13 family.
genes like me logo Genes that share domains with VPS13C: view

Function for VPS13C Gene

Molecular function for VPS13C Gene

UniProtKB/Swiss-Prot Function:
Necessary for proper mitochondrial function and maintenance of mitochondrial transmembrane potential. Involved in the regulation of PINK1/PRKN-mediated mitophagy in response to mitochondrial depolarization.

Phenotypes From GWAS Catalog for VPS13C Gene

genes like me logo Genes that share phenotypes with VPS13C: view

Human Phenotype Ontology for VPS13C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VPS13C Gene

MGI Knock Outs for VPS13C:
  • Vps13c Vps13c<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS13C

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for VPS13C Gene

Localization for VPS13C Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS13C Gene

Mitochondrion outer membrane.

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 VPS13C gene
Compartment Confidence
extracellular 4
mitochondrion 4
cytosol 4
endoplasmic reticulum 2
endosome 2
lysosome 2
golgi apparatus 2
plasma membrane 1
cytoskeleton 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VPS13C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005737 cytoplasm TAS 20081857
GO:0005739 mitochondrion IEA --
GO:0005741 mitochondrial outer membrane IDA 26942284
GO:0005829 cytosol IDA 26942284
genes like me logo Genes that share ontologies with VPS13C: view

Pathways & Interactions for VPS13C Gene

PathCards logo

SuperPathways for VPS13C Gene

No Data Available

Interacting Proteins for VPS13C Gene

Gene Ontology (GO) - Biological Process for VPS13C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA 21873635
GO:0006895 Golgi to endosome transport TAS 20081857
GO:0007005 mitochondrion organization IBA,IMP 26942284
GO:0032868 response to insulin IEA --
GO:0045053 protein retention in Golgi apparatus IBA 21873635
genes like me logo Genes that share ontologies with VPS13C: view

No data available for Pathways by source and SIGNOR curated interactions for VPS13C Gene

Drugs & Compounds for VPS13C Gene

No Compound Related Data Available

Transcripts for VPS13C Gene

mRNA/cDNA for VPS13C Gene

4 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS13C

Alternative Splicing Database (ASD) splice patterns (SP) for VPS13C Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^
SP1:
SP2: - -
SP3:
SP4: - -
SP5:
SP6:

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49 ^ 50 ^ 51 ^ 52 ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

ExUns: 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60a · 60b ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66a · 66b ^ 67 ^ 68 ^ 69 ^ 70 ^ 71 ^ 72 ^ 73 ^ 74 ^ 75 ^ 76 ^
SP1: -
SP2: -
SP3: -
SP4: -
SP5:
SP6:

ExUns: 77 ^ 78 ^ 79 ^ 80 ^ 81 ^ 82 ^ 83a · 83b ^ 84 ^ 85 ^
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:

Relevant External Links for VPS13C Gene

GeneLoc Exon Structure for
VPS13C

Expression for VPS13C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS13C Gene

Protein differential expression in normal tissues from HIPED for VPS13C Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.9) and Lymph node (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS13C Gene



Protein tissue co-expression partners for VPS13C Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS13C

SOURCE GeneReport for Unigene cluster for VPS13C Gene:

Hs.511668

mRNA Expression by UniProt/SwissProt for VPS13C Gene:

Q709C8-VP13C_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for VPS13C Gene

  • Liver(4.4)
  • Nervous system(4)
  • Pancreas(3.1)
  • Adrenal gland(3)
  • Blood(2.7)
  • Muscle(2.3)
  • Skin(2.2)
  • Lung(2.2)
  • Kidney(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with VPS13C: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS13C Gene

Orthologs for VPS13C Gene

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

Orthologs for VPS13C Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia VPS13C 30 31
  • 99.4 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VPS13C 30 31
  • 91.07 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VPS13C 30 31
  • 89.67 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Vps13c 30 17 31
  • 84.42 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia VPS13C 31
  • 79 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia VPS13C 31
  • 54 (a)
OneToOne
Chicken
(Gallus gallus)
Aves VPS13C 30 31
  • 71.5 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia VPS13C 31
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vps13c 30
  • 65.85 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC798746 30
  • 62.01 (n)
CR388046.3 31
  • 59 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Vps13 31
  • 30 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea T08G11.1 31
  • 29 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 31
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 31 (a)
OneToMany
Species where no ortholog for VPS13C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 VPS13C Gene

ENSEMBL:
Gene Tree for VPS13C (if available)
TreeFam:
Gene Tree for VPS13C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS13C: view image

Paralogs for VPS13C Gene

Paralogs for VPS13C Gene

(1) SIMAP similar genes for VPS13C Gene using alignment to 1 proteins:

  • VP13C_HUMAN
genes like me logo Genes that share paralogs with VPS13C: view

Variants for VPS13C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS13C Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
708604 Likely Benign: not provided 61,920,268(-) C/T MISSENSE_VARIANT
709146 Benign: not provided 61,915,840(-) T/C SYNONYMOUS_VARIANT
709147 Benign: not provided 61,949,492(-) G/A SYNONYMOUS_VARIANT
710295 Benign: not provided 61,951,941(-) T/G SYNONYMOUS_VARIANT
710296 Likely Benign: not provided 61,984,980(-) G/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for VPS13C Gene

Structural Variations from Database of Genomic Variants (DGV) for VPS13C Gene

Variant ID Type Subtype PubMed ID
dgv152n21 CNV gain 19592680
dgv4563n54 CNV gain 21841781
dgv4564n54 CNV loss 21841781
dgv744e212 CNV loss 25503493
esv1275705 CNV insertion 17803354
esv2582405 CNV deletion 19546169
esv2749762 CNV deletion 23290073
esv3306269 CNV mobile element insertion 20981092
esv3407880 CNV insertion 20981092
esv3892707 CNV loss 25118596
nsv1076412 CNV duplication 25765185
nsv1108961 CNV deletion 24896259
nsv1119445 CNV insertion 24896259
nsv1141265 CNV duplication 24896259
nsv457176 CNV gain 19166990
nsv457177 CNV loss 19166990
nsv457178 CNV loss 19166990
nsv471247 CNV gain 18288195
nsv481032 CNV novel sequence insertion 20440878
nsv521334 CNV loss 19592680
nsv569641 CNV loss 21841781
nsv569642 CNV loss 21841781
nsv569644 CNV loss 21841781
nsv569645 CNV loss 21841781
nsv569647 CNV loss 21841781
nsv569648 CNV loss 21841781
nsv569652 CNV loss 21841781
nsv827348 CNV gain 20364138

Variation tolerance for VPS13C Gene

Residual Variation Intolerance Score: 0.759% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.06; 93.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS13C Gene

Human Gene Mutation Database (HGMD)
VPS13C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS13C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS13C Gene

Disorders for VPS13C Gene

MalaCards: The human disease database

(9) MalaCards diseases for VPS13C Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

VP13C_HUMAN
  • Parkinson disease 23, autosomal recessive, early onset (PARK23) [MIM:616840]: An autosomal recessive, early-onset form of Parkinson disease, a complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability, as well as by a clinically significant response to treatment with levodopa. The pathology involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. {ECO:0000269 PubMed:26942284}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VPS13C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with VPS13C: view

No data available for Genatlas for VPS13C Gene

Publications for VPS13C Gene

  1. Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy. (PMID: 26942284) Lesage S … International Parkinson's Disease Genomics Consortium (IPDGC) (American journal of human genetics 2016) 3 4
  2. Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. (PMID: 20081857) Saxena R … Watanabe RM (Nature genetics 2010) 3 41
  3. Analysis of the human VPS13 gene family. (PMID: 15498460) Velayos-Baeza A … Monaco AP (Genomics 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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

Products for VPS13C Gene

Sources for VPS13C Gene