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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
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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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