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    SNX15 sorting nexin 15 [ Homo sapiens (human) ]

    Gene ID: 29907, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SNX15provided by HGNC
    Official Full Name
    sorting nexin 15provided by HGNC
    Primary source
    HGNC:HGNC:14978
    See related
    Ensembl:ENSG00000110025 MIM:605964; AllianceGenome:HGNC:14978
    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
    HSAF001435
    Summary
    This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. Overexpression of this gene results in a decrease in the processing of insulin and hepatocyte growth factor receptors to their mature subunits. This decrease is caused by the mislocalization of furin, the endoprotease responsible for cleavage of insulin and hepatocyte growth factor receptors. This protein is involved in endosomal trafficking from the plasma membrane to recycling endosomes or the trans-Golgi network. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream ADP-ribosylation factor-like 2 (ARL2) gene. [provided by RefSeq, Dec 2010]
    Expression
    Ubiquitous expression in fat (RPKM 9.4), kidney (RPKM 8.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX15 in Genome Data Viewer
    Location:
    11q13.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65027439..65040572)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65020701..65033855)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64794911..64808044)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ARL2-SNX15 readthrough (NMD candidate) Neighboring gene ADP ribosylation factor like GTPase 2 Neighboring gene microRNA 6879 Neighboring gene Sharpr-MPRA regulatory region 4003 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64811302-64811848 Neighboring gene SAC3 domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64814570-64815448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64815449-64816327 Neighboring gene N-acetylated alpha-linked acidic dipeptidase like 1 Neighboring gene Sharpr-MPRA regulatory region 288 Neighboring gene cell division cycle associated 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64846103-64846604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4939

    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. A clinical, genetic and candidate gene study of Silver syndrome, a complicated form of hereditary spastic paraplegia. Warner TT, et al. J Neurol, 2004 Sep. PMID 15372247
    2. Overexpression of a novel sorting nexin, SNX15, affects endosome morphology and protein trafficking. Barr VA, et al. Traffic, 2000 Nov. PMID 11208079
    3. Identification and characterization of SNX15, a novel sorting nexin involved in protein trafficking. Phillips SA, et al. J Biol Chem, 2001 Feb 16. PMID 11085978
    4. SNX15 links clathrin endocytosis to the PtdIns3P early endosome independently of the APPL1 endosome. Danson C, et al. J Cell Sci, 2013 Nov 1. PMID 23986476, Free PMC Article
    5. The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. Ciccarelli FD, et al. Genomics, 2003 Apr. PMID 12676568

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNX15 regulates the recycling of APP to cell surface and, thus, its processing for Abeta generation.
      Title: SNX15 Regulates Cell Surface Recycling of APP and Aβ Generation.
    2. The activated EGF receptor enters distinct sub-populations of SNX15- and APPL1-labelled peripheral endocytic vesicles.
      Title: SNX15 links clathrin endocytosis to the PtdIns3P early endosome independently of the APPL1 endosome.
    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

    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

    Readthrough ARL2-SNX15

    Readthrough gene: ARL2-SNX15, Included gene: ARL2

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-15
    Names
    clone iota unknown 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.

    Genomic

    1. NG_029947.2 RefSeqGene

      Range
      5002..18135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_013306.5 → NP_037438.2  sorting nexin-15 isoform A

      See identical proteins and their annotated locations for NP_037438.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A, also known as SNX15) represents the longer transcript and encodes the longer isoform (A).
      Source sequence(s)
      AP000436, AP003068
      Consensus CDS
      CCDS8089.1
      UniProtKB/Swiss-Prot
      E5KQS6, Q9NRS5, Q9NRS6
      UniProtKB/TrEMBL
      B3KU31, E5KQS5
      Related
      ENSP00000366452.3, ENST00000377244.8
      Conserved Domains (2) summary
      cd02677
      Location:267 → 341
      MIT_SNX15; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
      cl02563
      Location:9 → 126
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    2. NM_147777.4 → NP_680086.2  sorting nexin-15 isoform B

      See identical proteins and their annotated locations for NP_680086.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B, also known as SNX15A) lacks an alternate in-frame exon in the 3' coding region, compared to variant A, resulting in an isoform (B) that is shorter than isoform A.
      Source sequence(s)
      AP000436, AP003068
      Consensus CDS
      CCDS8090.1
      UniProtKB/TrEMBL
      E9PMW6
      Related
      ENSP00000316410.5, ENST00000352068.5
      Conserved Domains (2) summary
      cl00299
      Location:182 → 255
      MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...
      cl02563
      Location:9 → 126
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      65027439..65040572
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      65020701..65033855
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NRS6.1 GenPept UniProtKB/Swiss-Prot:Q9NRS6

    Gene LinkOut

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

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