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Aliases for VPS13C Gene

Aliases for VPS13C Gene

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

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 10. An important paralog of this gene is VPS13A.

UniProtKB/Swiss-Prot 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.

Additional gene information for VPS13C Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS13C Gene

Genomics for VPS13C Gene

GeneHancer (GH) Regulatory Elements for VPS13C Gene

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
GH15I062059 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 563.8 +0.2 185 2.6 PKNOX1 MLX ARID4B SIN3A DMAP1 POLR2B CBX5 ZNF207 ZNF143 DEK VPS13C LOC101928907 C2CD4A GC15P061947
GH15I062811 Enhancer 0.9 ENCODE 51.8 -751.7 -751734 2.4 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 ETS1 ZNF213 FOS ZC3H11A VPS13C USP3 USP3-AS1 LOC105370854 MIR190A GC15M063885 TLN2
GH15I063037 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.5 -986.9 -986934 20.2 ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 ZC3H11A MEF2D TPM1 TPM1-AS GC15P068650 GC15P069319 RPS27L VPS13C USP3 RAB8B LACTB GC15P069490
GH15I062134 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.7 -76.5 -76462 4.1 MZF1 FEZF1 SCRT2 RCOR1 KLF7 DEK EGR2 ZNF680 USF2 ZC3H11A VPS13C C2CD4B GC15P062091
GH15I062035 Enhancer 0.5 ENCODE 26.3 +24.8 24763 1.2 JUND POLR2A JUN PRDM1 VPS13C LOC101928907 GC15P061947
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VPS13C on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS13C gene promoter:

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)

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=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA92659.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; 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 posLast=578578, posLast=21552155, isoforms=2, 3, 42233, posLast=23042304, posLast=23572357, posLast=27772777, isoforms=2, 3, 43487, isoforms=2, 3, 43496, posLast=35013501, and posLast=35573557

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

Suggested Antigen Peptide Sequences for VPS13C Gene

GenScript: Design optimal peptide antigens:

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:

Animal Model Products

CRISPR Products

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 5
mitochondrion 5
cytosol 5
nucleus 1
endoplasmic reticulum 1
golgi apparatus 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:0005737 cytoplasm TAS 20081857
GO:0005739 mitochondrion IEA --
GO:0005741 mitochondrial outer membrane IDA 26942284
GO:0005829 cytosol IDA 26942284
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with VPS13C: view

Pathways & Interactions for VPS13C Gene

SuperPathways for VPS13C Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS13C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006895 Golgi to endosome transport TAS 20081857
GO:0007005 mitochondrion organization IMP 26942284
GO:1905090 negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization IMP 26942284
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

Unigene Clusters for VPS13C Gene

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

CRISPR Products

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
ECgene alternative splicing isoforms for
VPS13C

Expression for VPS13C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for VPS13C Gene



Protein tissue co-expression partners for VPS13C Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS13C Gene:

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(4.3)
  • Nervous system(3.4)
  • Pancreas(2.9)
  • Adrenal gland(2.6)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with VPS13C: 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 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 33 34
  • 99.4 (n)
dog
(Canis familiaris)
Mammalia VPS13C 33 34
  • 91.07 (n)
cow
(Bos Taurus)
Mammalia VPS13C 33 34
  • 89.67 (n)
mouse
(Mus musculus)
Mammalia Vps13c 33 16 34
  • 84.42 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS13C 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS13C 34
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS13C 33 34
  • 71.5 (n)
lizard
(Anolis carolinensis)
Reptilia VPS13C 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps13c 33
  • 65.85 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC798746 33
  • 62.01 (n)
CR388046.3 34
  • 59 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Vps13 34
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T08G11.1 34
  • 29 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS13 34
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 31 (a)
OneToMany
Species where no ortholog for VPS13C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for VPS13C Gene

Paralogs for VPS13C Gene

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

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

Variants for VPS13C Gene

Sequence variations from dbSNP and Humsavar for VPS13C Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs369100678 pathogenic, Parkinson disease 23, autosomal recessive early-onset, Parkinson disease, Parkinson disease 23, autosomal recessive, early onset (PARK23) [MIM:616840] 61,958,608(-) C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs869312809 pathogenic, Parkinson disease 23, autosomal recessive early-onset, Parkinson disease 61,915,631(-) A/C genic_downstream_transcript_variant, splice_donor_variant
rs869312810 pathogenic, Parkinson disease 23, autosomal recessive early-onset, Parkinson disease 61,882,652(-) C/A coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs869312811 pathogenic, Parkinson disease 23, autosomal recessive early-onset, Parkinson disease 61,947,292(-) GGG/GG coding_sequence_variant, frameshift, non_coding_transcript_variant
rs869320761 pathogenic, Parkinson disease 23, autosomal recessive early-onset 62,013,059(-) TCTG/TCTGTCTG coding_sequence_variant, frameshift, non_coding_transcript_variant

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

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

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

(5) MalaCards diseases for VPS13C Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, 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
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 58
  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 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Analysis of the human VPS13 gene family. (PMID: 15498460) Velayos-Baeza A … Monaco AP (Genomics 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 VPS13C Gene

Sources for VPS13C Gene

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