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

    Gene ID: 54832, updated on 10-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 9.0), spleen (RPKM 8.6) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (10 hits/1273 screens)

    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

    Interactions

    General gene information

    Clone Names

    • FLJ21361, DKFZp686E0570

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Golgi to endosome transport PubMed 
    involved_in lipid transport  
    involved_in mitochondrion organization  
    involved_in mitochondrion organization PubMed 
    involved_in negative regulation of type 2 mitophagy PubMed 
    involved_in protein retention in Golgi apparatus  
    involved_in protein targeting to vacuole  
    involved_in response to insulin  
    Component Evidence Code Pubs
    located_in cytoplasm PubMed 
    located_in cytosol PubMed 
    located_in dense core granule membrane  
    located_in endoplasmic reticulum membrane PubMed 
    located_in extracellular exosome PubMed 
    located_in late endosome PubMed 
    located_in late endosome membrane  
    located_in lipid droplet PubMed 
    located_in lysosomal membrane  
    located_in lysosome PubMed 
    located_in mitochondrial outer membrane PubMed 

    General protein information

    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)

    NEW Try the new Transcript table

    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

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