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SNX18 sorting nexin 18 [ Homo sapiens (human) ]

Gene ID: 112574, updated on 27-Nov-2024

Summary

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Official Symbol
SNX18provided by HGNC
Official Full Name
sorting nexin 18provided by HGNC
Primary source
HGNC:HGNC:19245
See related
Ensembl:ENSG00000178996 MIM:621000; AllianceGenome:HGNC:19245
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
SNAG1; SH3PX2; SH3PXD3B
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. This protein does not contain a coiled coil region, like some family members, but contains a SH3 domain. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 13.6), ovary (RPKM 10.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SNX18 in Genome Data Viewer
Location:
5q11.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (54517759..54648005)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (55345475..55475784)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (53813589..53842416)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1033 Neighboring gene ribosomal protein L37 pseudogene 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:53735813-53736314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22550 Neighboring gene heat shock protein family B (small) member 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:53813343-53813584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:53814497-53815441 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:53935341-53935915 Neighboring gene long intergenic non-protein coding RNA 2998 Neighboring gene uncharacterized LOC105378969 Neighboring gene NFE2L2 motif-containing MPRA enhancer 222 Neighboring gene chondroitin sulfate proteoglycan family member 4B, pseudogene Neighboring gene zinc finger protein 561-like

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. SNX18 is an SNX9 paralog that acts as a membrane tubulator in AP-1-positive endosomal trafficking. Håberg K, et al. J Cell Sci, 2008 May 1. PMID 18411244
  2. Mib1 modulates dynamin 2 recruitment via Snx18 to promote Dll1 endocytosis for efficient Notch signaling. Okano M, et al. Genes Cells, 2016 May. PMID 26923255
  3. Interaction between FIP5 and SNX18 regulates epithelial lumen formation. Willenborg C, et al. J Cell Biol, 2011 Oct 3. PMID 21969467, Free PMC Article
  4. SNX18 regulates ATG9A trafficking from recycling endosomes by recruiting Dynamin-2. Søreng K, et al. EMBO Rep, 2018 Apr. PMID 29437695, Free PMC Article
  5. FIP5 phosphorylation during mitosis regulates apical trafficking and lumenogenesis. Li D, et al. EMBO Rep, 2014 Apr. PMID 24591568, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. We propose a model where upon autophagy induction, SNX18 recruits Dynamin-2 to induce budding of ATG9A and ATG16L1 containing membranes from recycling endosomes that traffic to sites of autophagosome formation.
    Title: SNX18 regulates ATG9A trafficking from recycling endosomes by recruiting Dynamin-2.
  2. SNX18 promotes autophagosome formation by virtue of its ability to remodel membranes and provide membrane to forming autophagosomes.
    Title: Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation.
  3. The sorting nexin 9 (SNX9) subfamily members - SNX9, SNX18 and SNX33 - are required for progression and completion of mitosis.
    Title: SNX9, SNX18 and SNX33 are required for progression through and completion of mitosis.
  4. FIP5-SNX18 complex plays a pivotal role in the polarized transport of apical proteins during apical lumen initiation in epithelial cells.
    Title: Interaction between FIP5 and SNX18 regulates epithelial lumen formation.
  5. functions in multiple pathways of endocytosis at the plasma membrane
    Title: SNX18 shares a redundant role with SNX9 and modulates endocytic trafficking at the plasma membrane.
  6. The results indicate that SNX9-family members make up discrete membrane-scission units together with dynamin, and suggest that SNX18 mediates budding of carriers for AP-1-positive endosomal trafficking.
    Title: SNX18 is an SNX9 paralog that acts as a membrane tubulator in AP-1-positive endosomal trafficking.
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

EBI GWAS Catalog

Description
Genome-wide association study of antibody response to smallpox vaccine.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Viral bimolecular fluorescence complementation assay demonstrates the association of HIV-1 Nef with SNX18 in cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11997, FLJ32560, FLJ61062, MGC150827, MGC150829

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-4,5-bisphosphate 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 cleavage furrow formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cleavage furrow formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endocytosis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitotic cytokinesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in plasma membrane tubulation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in extracellular exosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in recycling endosome membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
sorting nexin-18
Names
SH3 and PX domain-containing protein 3B
sorting nexin associated golgi protein 1
sorting nexin-associated Golgi protein 1

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_001102575.2 → NP_001096045.1  sorting nexin-18 isoform a

    See identical proteins and their annotated locations for NP_001096045.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform (a).
    Source sequence(s)
    AC091888, AI335241, AI669182, AK022059, BC060791, BJ990551, CD722181
    Consensus CDS
    CCDS43317.1
    UniProtKB/Swiss-Prot
    Q96RF0
    Related
    ENSP00000370817.4, ENST00000381410.5
    Conserved Domains (3) summary
    cd07286
    Location:276 → 403
    PX_SNX18; The phosphoinositide binding Phox Homology domain of Sorting Nexin 18
    cd07670
    Location:415 → 621
    BAR_SNX18; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 18
    cd11897
    Location:4 → 58
    SH3_SNX18; Src Homology 3 domain of Sorting nexin 18

  2. NM_001145427.2 → NP_001138899.1  sorting nexin-18 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate donor splice site at the first coding exon compared to transcript variant 1. This results in a frame-shift, early translation termination, and an isoform (c) with a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC091888, AI335241, AK022059, AK304195, BC060791, BC117220, BJ990552, CN360136
    Consensus CDS
    CCDS54851.1
    UniProtKB/Swiss-Prot
    Q96RF0
    Related
    ENSP00000317332.4, ENST00000326277.5
    Conserved Domains (4) summary
    cd07286
    Location:276 → 403
    PX_SNX18; The phosphoinositide binding Phox Homology domain of Sorting Nexin 18
    cd11897
    Location:4 → 58
    SH3_SNX18; Src Homology 3 domain of Sorting nexin 18
    pfam12316
    Location:79 → 222
    Dsh_C; Segment polarity protein dishevelled (Dsh) C terminal
    cl12013
    Location:415 → 541
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  3. NM_052870.4 → NP_443102.2  sorting nexin-18 isoform b

    See identical proteins and their annotated locations for NP_443102.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice pattern in the 3' coding region compared to variant 1. The resulting protein (isoform b) has a longer and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC091888, AF395536, BC060791, BC117220, CN479485
    Consensus CDS
    CCDS3962.1
    UniProtKB/Swiss-Prot
    B4E2B3, H7BXX3, Q05BB3, Q0VG02, Q96RF0
    Related
    ENSP00000342276.7, ENST00000343017.11
    Conserved Domains (3) summary
    cd07286
    Location:276 → 403
    PX_SNX18; The phosphoinositide binding Phox Homology domain of Sorting Nexin 18
    cd11897
    Location:4 → 58
    SH3_SNX18; Src Homology 3 domain of Sorting nexin 18
    cl12013
    Location:415 → 541
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    54517759..54648005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008997.2 → XP_016864486.1  sorting nexin-18 isoform X2

    Conserved Domains (3) summary
    cd07286
    Location:276 → 403
    PX_SNX18; The phosphoinositide binding Phox Homology domain of Sorting Nexin 18
    cd11897
    Location:4 → 58
    SH3_SNX18; Src Homology 3 domain of Sorting nexin 18
    cl12013
    Location:415 → 541
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  2. XM_047416679.1 → XP_047272635.1  sorting nexin-18 isoform X1

RNA

  1. XR_007058577.1 RNA Sequence

  2. XR_001741987.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    55345475..55475784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351529.1 → XP_054207504.1  sorting nexin-18 isoform X1

  2. XM_054351530.1 → XP_054207505.1  sorting nexin-18 isoform X2

RNA

  1. XR_008487078.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96RF0.2 GenPept UniProtKB/Swiss-Prot:Q96RF0

Gene LinkOut

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