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VPS13C vacuolar protein sorting 13 homolog C [ Homo sapiens (human) ]

Gene ID: 54832, updated on 3-Nov-2024

Summary

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Official Symbol
VPS13Cprovided by HGNC
Official Full Name
vacuolar protein sorting 13 homolog Cprovided by HGNC
Primary source
HGNC:HGNC:23594
See related
Ensembl:ENSG00000129003 MIM:608879; AllianceGenome:HGNC:23594
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BLTP5C; PARK23
Summary
Involved in mitochondrion organization and negative regulation of type 2 mitophagy. Located in several cellular components, including late endosome; lipid droplet; and mitochondrial outer membrane. Implicated in Parkinson's disease 23. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 9.0), spleen (RPKM 8.6) and 25 other tissues See more
Orthologs
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Genomic context

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See VPS13C in Genome Data Viewer
Location:
15q22.2
Exon count:
88
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (61852389..62060447, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (59655984..59864419, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (62144588..62352646, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984782 Neighboring gene uncharacterized LOC107984783 Neighboring gene long intergenic non-protein coding RNA 2349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:62119811-62120312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:62120313-62120812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:62122812-62123677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:62123678-62124542 Neighboring gene uncharacterized LOC124903501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:62359400-62359915 Neighboring gene Sharpr-MPRA regulatory region 14002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6502 Neighboring gene VPS13C divergent transcript Neighboring gene C2 calcium dependent domain containing 4A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Mutation screening and burden analysis of VPS13C in Chinese patients with early-onset Parkinson's disease. Gu X, et al. Neurobiol Aging, 2020 Oct. PMID 32507414
  2. Familial dementia with Lewy bodies with VPS13C mutations. Kobayashi R, et al. Parkinsonism Relat Disord, 2020 Dec. PMID 33039764
  3. Contribution of rare homozygous and compound heterozygous VPS13C missense mutations to dementia with Lewy bodies and Parkinson's disease. Smolders S, et al. Acta Neuropathol Commun, 2021 Feb 12. PMID 33579389, Free PMC Article
  4. Association between VPS13C rs2414739 polymorphism and Parkinson's disease risk: A meta-analysis. Bai X, et al. Neurosci Lett, 2021 May 29. PMID 33838259
  5. Identification of a large homozygous VPS13C deletion in a patient with early-onset Parkinsonism. Darvish H, et al. Mov Disord, 2018 Dec. PMID 30452786, Free PMC Article

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VPS13C and STING expression in neuropsychiatric systemic lupus erythematosus: unveiling an unbreached territory.
    Title: VPS13C and STING expression in neuropsychiatric systemic lupus erythematosus: unveiling an unbreached territory.
  2. VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons.
    Title: VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons.
  3. In situ architecture of the lipid transport protein VPS13C at ER-lysosome membrane contacts.
    Title: In situ architecture of the lipid transport protein VPS13C at ER-lysosome membrane contacts.
  4. ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
    Title: ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
  5. VPS13C-associated Parkinson's disease: Two novel cases and review of the literature.
    Title: VPS13C-associated Parkinson's disease: Two novel cases and review of the literature.
  6. Familial dementia with Lewy bodies with VPS13C mutations.
    Title: Familial dementia with Lewy bodies with VPS13C mutations.
  7. Association between VPS13C rs2414739 polymorphism and Parkinson's disease risk: A meta-analysis.
    Title: Association between VPS13C rs2414739 polymorphism and Parkinson's disease risk: A meta-analysis.
  8. Contribution of rare homozygous and compound heterozygous VPS13C missense mutations to dementia with Lewy bodies and Parkinson's disease.
    Title: Contribution of rare homozygous and compound heterozygous VPS13C missense mutations to dementia with Lewy bodies and Parkinson's disease.
  9. Mutation screening and burden analysis of VPS13C in Chinese patients with early-onset Parkinson's disease.
    Title: Mutation screening and burden analysis of VPS13C in Chinese patients with early-onset Parkinson's disease.
  10. TBC1D1 interacting proteins, VPS13A and VPS13C, regulate GLUT4 homeostasis in C2C12 myotubes.
    Title: TBC1D1 interacting proteins, VPS13A and VPS13C, regulate GLUT4 homeostasis in C2C12 myotubes.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive early-onset Parkinson disease 23
MedGen: C4225186 OMIM: 616840 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
EBI GWAS Catalog
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.
EBI GWAS Catalog
Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.
EBI GWAS Catalog
Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21361, DKFZp686E0570

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in Golgi to endosome transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in lipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in mitochondrion organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of type 2 mitophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein retention in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to insulin IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dense core granule membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lysosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial outer membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
intermembrane lipid transfer protein VPS13C
Names
bridge-like lipid transfer protein family member 5C
vacuolar protein sorting-associated protein 13C

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_027782.1 RefSeqGene

    Range
    5019..213077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001018088.3 → NP_001018098.1  intermembrane lipid transfer protein VPS13C isoform 2B

    See identical proteins and their annotated locations for NP_001018098.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2B) differs in the 3' UTR and 3' coding region, compared to variant 2A. The resulting isoform (2B) has a distinct C-terminus and is shorter than isoform 2A.
    Source sequence(s)
    AC009554, AJ626861, H05069
    Consensus CDS
    CCDS45272.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000496179.1, ENST00000645819.1
    Conserved Domains (8) summary
    COG5043
    Location:1046 → 2612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2764 → 3016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3507 → 3582
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185 → 413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:3323 → 3500
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:613 → 833
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:3116 → 3181
    WWE; WWE domain

  2. NM_017684.5 → NP_060154.3  intermembrane lipid transfer protein VPS13C isoform 1A

    See identical proteins and their annotated locations for NP_060154.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1A) lacks an in-frame exon in the coding region, compared to variant 2A. The encoded isoform (1A) is shorter than isoform 2A.
    Source sequence(s)
    AJ608770, AK000143
    Consensus CDS
    CCDS10180.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000249837.3, ENST00000249837.7
    Conserved Domains (8) summary
    COG5043
    Location:1003 → 2569
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2721 → 2973
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3464 → 3539
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 370
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:3280 → 3457
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 790
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:3073 → 3138
    WWE; WWE domain

  3. NM_018080.4 → NP_060550.2  intermembrane lipid transfer protein VPS13C isoform 1B

    See identical proteins and their annotated locations for NP_060550.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1B) differs in the 3' UTR and has multiple coding region differences, compared to variant 2A. The resulting isoform (1B) has a distinct C-terminus and is shorter than isoform 2A.
    Source sequence(s)
    AC009554, AJ626860, H05069
    Consensus CDS
    CCDS58367.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000379235.3, ENST00000395898.3
    Conserved Domains (8) summary
    COG5043
    Location:1003 → 2569
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2721 → 2973
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3464 → 3539
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142 → 370
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:3280 → 3457
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570 → 790
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:3073 → 3138
    WWE; WWE domain

  4. NM_020821.3 → NP_065872.1  intermembrane lipid transfer protein VPS13C isoform 2A

    See identical proteins and their annotated locations for NP_065872.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2A) encodes the longest isoform (2A).
    Source sequence(s)
    AJ608771, AK000143
    Consensus CDS
    CCDS32257.1
    UniProtKB/Swiss-Prot
    Q6ISR4, Q702P2, Q702P3, Q709C8, Q709C9, Q9NXN8, Q9P2C6
    Related
    ENSP00000493560.2, ENST00000644861.2
    Conserved Domains (8) summary
    COG5043
    Location:1046 → 2612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2764 → 3016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3507 → 3582
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185 → 413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:3323 → 3500
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:613 → 833
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:3116 → 3181
    WWE; WWE domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    61852389..62060447 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432741.1 → XP_047288697.1  intermembrane lipid transfer protein VPS13C isoform X1

  2. XM_011521713.4 → XP_011520015.1  intermembrane lipid transfer protein VPS13C isoform X1

    Conserved Domains (5) summary
    COG5043
    Location:1046 → 2612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:2764 → 3016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185 → 413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16910
    Location:613 → 833
    VPS13_mid_rpt; Repeating coiled region of VPS13

  3. XM_047432742.1 → XP_047288698.1  intermembrane lipid transfer protein VPS13C isoform X3

  4. XM_011521714.3 → XP_011520016.1  intermembrane lipid transfer protein VPS13C isoform X2

    Conserved Domains (3) summary
    pfam12624
    Location:4 → 113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185 → 413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16910
    Location:613 → 833
    VPS13_mid_rpt; Repeating coiled region of VPS13

RNA

  1. XR_007064464.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    59655984..59864419 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378266.1 → XP_054234241.1  intermembrane lipid transfer protein VPS13C isoform X1

  2. XM_054378267.1 → XP_054234242.1  intermembrane lipid transfer protein VPS13C isoform X1

  3. XM_054378269.1 → XP_054234244.1  intermembrane lipid transfer protein VPS13C isoform X3

  4. XM_054378268.1 → XP_054234243.1  intermembrane lipid transfer protein VPS13C isoform X2

RNA

  1. XR_008488972.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q709C8.1 GenPept UniProtKB/Swiss-Prot:Q709C8

Gene LinkOut

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