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SNX17 sorting nexin 17 [ Homo sapiens (human) ]

Gene ID: 9784, updated on 11-Apr-2024

Summary

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Official Symbol
SNX17provided by HGNC
Official Full Name
sorting nexin 17provided by HGNC
Primary source
HGNC:HGNC:14979
See related
Ensembl:ENSG00000115234 MIM:605963; AllianceGenome:HGNC:14979
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
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 B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]
Expression
Ubiquitous expression in spleen (RPKM 29.0), lymph node (RPKM 26.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SNX17 in Genome Data Viewer
Location:
2p23.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (27370616..27377535)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (27413013..27419930)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27593483..27600402)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene general transcription factor IIIC subunit 2 Neighboring gene GTF3C2 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:27579025-27579638 and GRCh37_chr2:27579639-27580252 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27582391-27583132 Neighboring gene GTF3C2 antisense RNA 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27592451-27593412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27593413-27594374 Neighboring gene eukaryotic translation initiation factor 2B subunit delta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27601343-27602213 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11297 Neighboring gene zinc finger protein 513 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27618171-27618672 Neighboring gene ferritin heavy chain 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15507 Neighboring gene nuclear receptor binding protein 1

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. SNX17 affects T cell activation by regulating TCR and integrin recycling. Osborne DG, et al. J Immunol, 2015 May 1. PMID 25825439, Free PMC Article
  2. SNX17 facilitates infection with diverse papillomavirus types. Bergant M, et al. J Virol, 2013 Jan. PMID 23115288, Free PMC Article
  3. Human papillomavirus L2 facilitates viral escape from late endosomes via sorting nexin 17. Bergant Marušič M, et al. Traffic, 2012 Mar. PMID 22151726, Free PMC Article
  4. Adaptor protein sorting nexin 17 interacts with the scavenger receptor FEEL-1/stabilin-1 and modulates its expression on the cell surface. Adachi H, et al. Biochim Biophys Acta, 2010 May. PMID 20226821
  5. Polarized traffic of LRP1 involves AP1B and SNX17 operating on Y-dependent sorting motifs in different pathways. Donoso M, et al. Mol Biol Cell, 2009 Jan. PMID 19005208, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Promotion of esophageal adenocarcinoma metastasis via Wnt/ss-catenin signal pathway by sorting nexins 3.
    Title: Promotion of esophageal adenocarcinoma metastasis via Wnt/ß-catenin signal pathway by sorting nexins 3.
  2. SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis.
    Title: SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis.
  3. HPV-16 L2 recruitment of SNX17 occurs prior to capsid disassembly.
    Title: Characterizing the spatio-temporal role of sorting nexin 17 in human papillomavirus trafficking.
  4. The double knockdown of SNX17 and SNX27 results in a striking reduction of papillomavirus 16 infection due to interruption of their binding to the L2 viral protein.
    Title: A Novel PDZ Domain Interaction Mediates the Binding between Human Papillomavirus 16 L2 and Sorting Nexin 27 and Modulates Virion Trafficking.
  5. SNX17 plays a role in the maintenance of normal surface levels of activating receptors and integrins to permit optimum T cell activation at the immune synapse.
    Title: SNX17 affects T cell activation by regulating TCR and integrin recycling.
  6. Data indicate that the major binding site for binding of sorting nexin 17 (SNX17) is confined to the NPXF2 motif in cytoplasmic adaptor protein Krev interaction trapped 1 (KRIT1).
    Title: Structural determinants for binding of sorting nexin 17 (SNX17) to the cytoplasmic adaptor protein Krev interaction trapped 1 (KRIT1).
  7. Sorting nexin 17 regulates ApoER2 recycling and reelin signaling.
    Title: Sorting nexin 17 regulates ApoER2 recycling and reelin signaling.
  8. The authors demonstrate that SNX17 is essential for infection with all papillomavirus types analyzed, indicating an evolutionarily highly conserved virus entry mechanism.
    Title: SNX17 facilitates infection with diverse papillomavirus types.
  9. depletion of SNX17 in HeLa cells resulted in lysosomal degradation of multiple members of the integrin family of extracellular matrix recep-tors.
    Title: SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways.
  10. SNX17 regulates amyloid precursor protein trafficking and processing in the early endosomes
    Title: Adaptor protein sorting nexin 17 regulates amyloid precursor protein trafficking and processing in the early endosomes.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Genetic variants associated with breast size also influence breast cancer risk.
EBI GWAS Catalog
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
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)

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

  • KIAA0064

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables low-density lipoprotein particle receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor binding NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in aorta development IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac septum development IEA
Inferred from Electronic Annotation
more info
  
involved_in cholesterol catabolic process IC
Inferred by Curator
more info
 PubMed 
involved_in coronary vasculature development IEA
Inferred from Electronic Annotation
more info
  
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 endosomal transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in kidney development IEA
Inferred from Electronic Annotation
more info
  
involved_in receptor-mediated endocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of endocytosis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome membrane IDA
Inferred from Direct Assay
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 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
sorting nexin-17

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_001267059.2 → NP_001253988.1  sorting nexin-17 isoform 2

    See identical proteins and their annotated locations for NP_001253988.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AC074117, AK300144
    UniProtKB/TrEMBL
    B4DE48, B4DTB8
    Conserved Domains (3) summary
    cd06885
    Location:2 → 94
    PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
    cd13337
    Location:257 → 376
    FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
    cl00155
    Location:104 → 174
    UBQ; Ubiquitin-like proteins

  2. NM_001267060.2 → NP_001253989.1  sorting nexin-17 isoform 3

    See identical proteins and their annotated locations for NP_001253989.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
    Source sequence(s)
    AC074117, AK298869
    Consensus CDS
    CCDS58704.1
    UniProtKB/TrEMBL
    B4DE48
    Related
    ENSP00000439208.1, ENST00000537606.5
    Conserved Domains (3) summary
    cd13337
    Location:244 → 363
    FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
    cl02563
    Location:2 → 81
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
    cl09511
    Location:94 → 226
    FERM_B-lobe; FERM domain B-lobe

  3. NM_001267061.2 → NP_001253990.1  sorting nexin-17 isoform 4

    See identical proteins and their annotated locations for NP_001253990.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon contains an alternate exon, lacks a portion of the 5' coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC074117, AK298620
    UniProtKB/TrEMBL
    B4DE48, B4DQ37
    Conserved Domains (3) summary
    cd06885
    Location:2 → 86
    PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
    cd13337
    Location:249 → 368
    FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
    cl00155
    Location:96 → 166
    UBQ; Ubiquitin-like proteins

  4. NM_014748.4 → NP_055563.1  sorting nexin-17 isoform 1

    See identical proteins and their annotated locations for NP_055563.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
    Source sequence(s)
    AC074117, D31764
    Consensus CDS
    CCDS1750.1
    UniProtKB/Swiss-Prot
    B4DQM7, Q15036, Q53HN7, Q6IAS3
    UniProtKB/TrEMBL
    B4DE48
    Related
    ENSP00000233575.2, ENST00000233575.7
    Conserved Domains (3) summary
    cd06885
    Location:2 → 106
    PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
    cd13337
    Location:269 → 388
    FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
    cl09511
    Location:119 → 251
    FERM_B-lobe; FERM domain B-lobe

RNA

  1. NR_049782.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, AK297054

  2. NR_049783.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, AK293252

  3. NR_049784.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, BC021108
    Related
    ENST00000427123.5

  4. NR_049785.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, AK308487
    Related
    ENST00000440760.5

  5. NR_049786.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks an alternate exon and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, AK298856

  6. NR_049787.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) lacks two alternate 5' exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, AK295278

  7. NR_049788.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) lacks three exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074117, BC032320

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    27370616..27377535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533203.3 → XP_011531505.1  sorting nexin-17 isoform X1

    See identical proteins and their annotated locations for XP_011531505.1

    UniProtKB/TrEMBL
    B4DDM3, B7ZAQ8
    Conserved Domains (2) summary
    cd13337
    Location:55 → 174
    FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
    cl09511
    Location:27 → 60
    FERM_B-lobe; FERM domain B-lobe

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    27413013..27419930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344758.1 → XP_054200733.1  sorting nexin-17 isoform X1

    UniProtKB/TrEMBL
    B4DDM3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15036.1 GenPept UniProtKB/Swiss-Prot:Q15036

Gene LinkOut

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