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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
    mouse all
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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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    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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