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

    Gene ID: 54832, updated on 7-Apr-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 parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization. Located in cytosol and mitochondrial outer membrane. Implicated in Parkinson's disease 23. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lymph node (RPKM 9.0), spleen (RPKM 8.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q22.2
    Exon count:
    88
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (61852389..62060447, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (59655984..59864419, complement)
    105.20220307 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
    • 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. In situ architecture of the lipid transport protein VPS13C at ER-lysosome membrane contacts. Cai S, et al. Proc Natl Acad Sci U S A, 2022 Jul 19. PMID 35858323, Free PMC Article
    2. VPS13C-associated Parkinson's disease: Two novel cases and review of the literature. Monfrini E, et al. Parkinsonism Relat Disord, 2022 Jan. PMID 34875562
    3. Association between VPS13C rs2414739 polymorphism and Parkinson's disease risk: A meta-analysis. Bai X, et al. Neurosci Lett, 2021 May 29. PMID 33838259
    4. 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
    5. Familial dementia with Lewy bodies with VPS13C mutations. Kobayashi R, et al. Parkinsonism Relat Disord, 2020 Dec. PMID 33039764

    See all (67) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons.
      Title: VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons.
    2. 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.
    3. 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.
    4. 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.
    5. Familial dementia with Lewy bodies with VPS13C mutations.
      Title: Familial dementia with Lewy bodies with VPS13C mutations.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. human VPS13A and VPS13C bind to the ER, tethering it to mitochondria (VPS13A), to late endosome/lysosomes (VPS13C), and to lipid droplets (both VPS13A and VPS13C).
      Title: VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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
    		Compare labs

    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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization 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_2023_10

    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

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