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VPS50 VPS50 subunit of EARP/GARPII complex [ Homo sapiens (human) ]

Gene ID: 55610, updated on 3-Nov-2024

Summary

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Official Symbol
VPS50provided by HGNC
Official Full Name
VPS50 subunit of EARP/GARPII complexprovided by HGNC
Primary source
HGNC:HGNC:25956
See related
Ensembl:ENSG00000004766 MIM:616465; AllianceGenome:HGNC:25956
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NEDMSC; VPS54L; CCDC132
Summary
Enables SNARE binding activity. Acts upstream of or within endocytic recycling. Located in recycling endosome. Part of EARP complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in brain (RPKM 5.6), thyroid (RPKM 4.2) and 25 other tissues See more
Orthologs
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Genomic context

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See VPS50 in Genome Data Viewer
Location:
7q21.2-q21.3
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (93232366..93361123)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (94474420..94603577)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (92861679..92990435)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26280 Neighboring gene sterile alpha motif domain containing 9 like Neighboring gene HEPACAM family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:92890341-92890842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:93025621-93026134 Neighboring gene calcitonin receptor Neighboring gene microRNA 653 Neighboring gene microRNA 489

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. Biallelic variants in VPS50 cause a neurodevelopmental disorder with neonatal cholestasis. Schneeberger PE, et al. Brain, 2021 Nov 29. PMID 34037727
  2. CCDC132 is highly expressed in atopic dermatitis T cells. Matsumoto Y, et al. Mol Med Rep, 2010 Jan-Feb. PMID 21472204
  3. A proposed clinical application of a model of CO2 laser radiation induced damage craters. Canestri F. J Med Eng Technol, 1988 May-Jun. PMID 3172165
  4. TSSC1 is novel component of the endosomal retrieval machinery. Gershlick DC, et al. Mol Biol Cell, 2016 Sep 15. PMID 27440922, Free PMC Article
  5. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, et al. Nat Cell Biol, 2015 May. PMID 25799061, Free PMC Article

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Biallelic variants in VPS50 cause a neurodevelopmental disorder with neonatal cholestasis.
    Title: Biallelic variants in VPS50 cause a neurodevelopmental disorder with neonatal cholestasis.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Submit: New GeneRIF Correction

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
Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
MedGen: C5562052 OMIM: 619685 GeneReviews: Not available
not available

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

  • FLJ20097, FLJ23581, KIAA1861, MGC176659

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SNARE binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within endocytic recycling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endocytic recycling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytic recycling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of EARP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of EARP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of EARP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in recycling endosome NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
syndetin
Names
EARP/GARPII complex subunit VPS50
VPS50, EARP/GARPII complex subunit
coiled-coil domain containing 132
coiled-coil domain-containing protein 132

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.

mRNA and Protein(s)

  1. NM_001257998.2 → NP_001244927.1  syndetin isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC002379, AC002453, AK126478, BE671517
    Consensus CDS
    CCDS59065.1
    UniProtKB/TrEMBL
    A7MD03
    Related
    ENSP00000443104.1, ENST00000544910.5
    Conserved Domains (2) summary
    pfam10474
    Location:696 → 927
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:24 → 315
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

  2. NM_017667.4 → NP_060137.2  syndetin isoform a

    See identical proteins and their annotated locations for NP_060137.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB100163, AC002379, BC017888, BC035984, BE671517
    Consensus CDS
    CCDS43617.1
    UniProtKB/Swiss-Prot
    B3KX22, D1MQ00, F5H5U7, Q75N07, Q8WVK3, Q96JG6, Q9H5C6
    UniProtKB/TrEMBL
    A7MD03
    Related
    ENSP00000307666.5, ENST00000305866.10
    Conserved Domains (2) summary
    pfam10474
    Location:726 → 957
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    pfam10475
    Location:54 → 345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)

  3. NM_024553.3 → NP_078829.1  syndetin isoform b

    See identical proteins and their annotated locations for NP_078829.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC002379, AC002453
    Consensus CDS
    CCDS5630.1
    UniProtKB/Swiss-Prot
    Q96JG6
    Related
    ENSP00000251739.5, ENST00000251739.9
    Conserved Domains (1) summary
    cl19297
    Location:54 → 314
    Dor1; Dor1-like family

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    93232366..93361123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516396.4 → XP_011514698.1  syndetin isoform X3

    Conserved Domains (2) summary
    pfam10475
    Location:54 → 345
    DUF2450; Protein of unknown function N-terminal domain (DUF2450)
    pfam13900
    Location:633 → 671
    GVQW; Putative domain of unknown function

  2. XM_047420601.1 → XP_047276557.1  syndetin isoform X4

  3. XM_011516395.3 → XP_011514697.1  syndetin isoform X1

    UniProtKB/TrEMBL
    A7MD03
    Conserved Domains (2) summary
    pfam10474
    Location:537 → 768
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    cl19297
    Location:1 → 156
    Dor1; Dor1-like family

  4. XM_024446826.2 → XP_024302594.1  syndetin isoform X2

    UniProtKB/TrEMBL
    B4DS55
    Conserved Domains (2) summary
    pfam10474
    Location:457 → 688
    DUF2451; Protein of unknown function C-terminus (DUF2451)
    cl19297
    Location:1 → 76
    Dor1; Dor1-like family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    94474420..94603577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358629.1 → XP_054214604.1  syndetin isoform X3

  2. XM_054358630.1 → XP_054214605.1  syndetin isoform X4

  3. XM_054358627.1 → XP_054214602.1  syndetin isoform X1

  4. XM_054358628.1 → XP_054214603.1  syndetin isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JG6.3 GenPept UniProtKB/Swiss-Prot:Q96JG6

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