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

Gene ID: 54832, updated on 5-Aug-2018

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; Vega:OTTHUMG00000132801
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
PARK23
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 9.0), spleen (RPKM 8.6) and 25 other tissues See more
Orthologs

Genomic context

See VPS13C in Genome Data Viewer
Location:
15q22.2
Exon count:
88
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (61852389..62060465, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (62144588..62352664, 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 uncharacterized LOC101928907 Neighboring gene C2 calcium dependent domain containing 4A

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21361, DKFZp686E0570

Gene Ontology Provided by GOA

Process Evidence Code Pubs
Golgi to endosome transport TAS
Traceable Author Statement
more info
PubMed 
mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein retention in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
extrinsic component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial outer membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 13C

NCBI Reference Sequences (RefSeq)

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
    5001..213077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001018088.2NP_001018098.1  vacuolar protein sorting-associated protein 13C 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, AC104590, AJ626861, H05069
    Consensus CDS
    CCDS45272.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000379233.4, OTTHUMP00000247224, ENST00000395896.8, OTTHUMT00000416000
    Conserved Domains (8) summary
    COG5043
    Location:10462612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27643016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:35073582
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:33233500
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:613833
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:31163181
    WWE; WWE domain
  2. NM_017684.4NP_060154.3  vacuolar protein sorting-associated protein 13C 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)
    AC104590, AJ608770, AK000143
    Consensus CDS
    CCDS10180.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000249837.3, OTTHUMP00000163686, ENST00000249837.7, OTTHUMT00000256218
    Conserved Domains (8) summary
    COG5043
    Location:10032569
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27212973
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:34643539
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142370
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:32803457
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570790
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:30733138
    WWE; WWE domain
  3. NM_018080.3NP_060550.2  vacuolar protein sorting-associated protein 13C 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, AC104590, AJ626860, H05069
    Consensus CDS
    CCDS58367.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000379235.3, OTTHUMP00000247225, ENST00000395898.3, OTTHUMT00000416001
    Conserved Domains (8) summary
    COG5043
    Location:10032569
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27212973
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:34643539
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:142370
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:32803457
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:570790
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:30733138
    WWE; WWE domain
  4. NM_020821.2NP_065872.1  vacuolar protein sorting-associated protein 13C 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)
    AC104590, AJ608771, AK000143
    Consensus CDS
    CCDS32257.1
    UniProtKB/Swiss-Prot
    Q709C8
    Related
    ENSP00000493560.1, OTTHUMP00000247223, ENST00000644861.1, OTTHUMT00000415997
    Conserved Domains (8) summary
    COG5043
    Location:10462612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27643016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:35073582
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16909
    Location:33233500
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    pfam16910
    Location:613833
    VPS13_mid_rpt; Repeating coiled region of VPS13
    cl02729
    Location:31163181
    WWE; WWE domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

    Range
    61852389..62060465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521713.3XP_011520015.1  vacuolar protein sorting-associated protein 13C isoform X1

    Conserved Domains (5) summary
    COG5043
    Location:10462612
    MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
    pfam06650
    Location:27643016
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16910
    Location:613833
    VPS13_mid_rpt; Repeating coiled region of VPS13
  2. XM_011521714.2XP_011520016.1  vacuolar protein sorting-associated protein 13C isoform X2

    Conserved Domains (3) summary
    pfam12624
    Location:4113
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16908
    Location:185413
    VPS13; Vacuolar sorting-associated protein 13, N-terminal
    pfam16910
    Location:613833
    VPS13_mid_rpt; Repeating coiled region of VPS13

RNA

  1. XR_001751332.1 RNA Sequence

  2. XR_931855.2 RNA Sequence

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