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    VPS35L VPS35 endosomal protein sorting factor like [ Homo sapiens (human) ]

    Gene ID: 57020, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VPS35Lprovided by HGNC
    Official Full Name
    VPS35 endosomal protein sorting factor likeprovided by HGNC
    Primary source
    HGNC:HGNC:24641
    See related
    Ensembl:ENSG00000103544 MIM:618981; AllianceGenome:HGNC:24641
    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
    EC97; RTSC3; C16orf62
    Summary
    Involved in Golgi to plasma membrane transport and endocytic recycling. Located in endosome. Implicated in Ritscher-Schinzel syndrome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 13.6), brain (RPKM 13.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS35L in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19555703..19701163)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19486575..19631965)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (19567025..19712485)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19532887-19533621 Neighboring gene glycerophosphodiester phosphodiesterase 1 Neighboring gene centriolar coiled-coil protein 110 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19566659-19567621 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:19620544-19621743 Neighboring gene NANOG hESC enhancer GRCh37_chr16:19673654-19674240 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19698132-19698632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710103-19710758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710759-19711413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721101-19721825 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721826-19722552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:19723278-19724003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10534 Neighboring gene lysine rich nucleolar protein 1 Neighboring gene IQ motif containing K Neighboring gene uncharacterized LOC105371115

    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. Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome. Otsuji S, et al. J Med Genet, 2023 Apr. PMID 36113987, Free PMC Article
    2. Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex. Kato K, et al. J Med Genet, 2020 Apr. PMID 31712251
    3. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Healy MD, et al. Cell, 2023 May 11. PMID 37172566, Free PMC Article
    4. Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. Naukkarinen J, et al. PLoS Genet, 2010 Jun 3. PMID 20532202, Free PMC Article
    5. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Phillips-Krawczak CA, et al. Mol Biol Cell, 2015 Jan 1. PMID 25355947, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome.
      Title: Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome.
    2. Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex.
      Title: Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex.
    3. Heterotrimer composed of DSCR3, C16orf62 and VPS29 orchestrates endosomal cargo retrieval and recycling.
      Title: Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.
    4. 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.
    5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Ritscher-Schinzel syndrome 3
    MedGen: C5436883 OMIM: 619135 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21040, MGC16824, DKFZp313M0539, DKFZp434B0212

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    VPS35 endosomal protein-sorting factor-like
    Names
    UPF0505 protein C16orf62
    esophageal cancer associated protein

    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_001300743.3 → NP_001287672.2  VPS35 endosomal protein-sorting factor-like isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621, AK095078
      Consensus CDS
      CCDS73840.1
      UniProtKB/TrEMBL
      B3KT69, F5H7K1
      Related
      ENSP00000442468.2, ENST00000542263.5

    2. NM_001365293.2 → NP_001352222.1  VPS35 endosomal protein-sorting factor-like isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621
      UniProtKB/TrEMBL
      B3KT69

    3. NM_001365294.2 → NP_001352223.1  VPS35 endosomal protein-sorting factor-like isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621
      UniProtKB/TrEMBL
      B3KT69

    4. NM_001365295.2 → NP_001352224.1  VPS35 endosomal protein-sorting factor-like isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621
      UniProtKB/TrEMBL
      H3BV68
      Related
      ENSP00000457973.1, ENST00000543152.5

    5. NM_020314.7 → NP_064710.5  VPS35 endosomal protein-sorting factor-like isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC002550, AK290286, AL136744, BP219237, DA452318
      Consensus CDS
      CCDS32397.3
      UniProtKB/Swiss-Prot
      A8K2M1, O43329, Q69YI1, Q6PDA0, Q7L371, Q7Z3J2, Q86W66, Q8WXA5, Q9H0L7, Q9H7C8
      UniProtKB/TrEMBL
      E7EWW0
      Related
      ENSP00000395973.3, ENST00000417362.7

    RNA

    1. NR_158160.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621

    2. NR_158161.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC002550, AC012621

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      19555703..19701163
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      19486575..19631965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3J2.2 GenPept UniProtKB/Swiss-Prot:Q7Z3J2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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