U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SNX5 sorting nexin 5 [ Homo sapiens (human) ]

Gene ID: 27131, updated on 2-Nov-2024

Summary

Go to the top of the page Help
Official Symbol
SNX5provided by HGNC
Official Full Name
sorting nexin 5provided by HGNC
Primary source
HGNC:HGNC:14969
See related
Ensembl:ENSG00000089006 MIM:605937; AllianceGenome:HGNC:14969
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 functions in endosomal sorting, the phosphoinositide-signaling pathway, and macropinocytosis. This gene may play a role in the tumorigenesis of papillary thyroid carcinoma. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in thyroid (RPKM 76.1), kidney (RPKM 52.7) and 24 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SNX5 in Genome Data Viewer
Location:
20p11.23
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (17941600..17968794, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (17992739..18019917, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (17922244..17949437, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17856497-17857399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17862693-17863606 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:17868266-17869465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17876154-17876830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17568 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:17887704-17887865 Neighboring gene RNA, U6 small nuclear 192, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17909901-17910427 Neighboring gene MPRA-validated peak4160 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17919356-17919949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17921137-17921728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948150-17948904 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948905-17949659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:17950167-17951366 Neighboring gene small nucleolar RNA, C/D box 17 Neighboring gene NANOG hESC enhancer GRCh37_chr20:17964055-17965008 Neighboring gene mitochondrial genome maintenance exonuclease 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17579 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:17980569-17981070 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17985803-17986364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988051-17988612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988613-17989173 Neighboring gene prothymosin alpha pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:18017759-18018259 Neighboring gene ovo like zinc finger 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:18034137-18034637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:18036965-18037752

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Upregulation of SNX5 predicts poor prognosis and promotes hepatocellular carcinoma progression by modulating the EGFR-ERK1/2 signaling pathway. Zhou Q, et al. Oncogene, 2020 Mar. PMID 31819169
  2. SNX5 promotes antigen presentation in B cells by dual regulation of actin and lysosomal dynamics. Cabrera-Reyes F, et al. Life Sci Alliance, 2025 Jan. PMID 39448266, Free PMC Article
  3. The phosphorylation of sorting nexin 5 at serine 226 regulates retrograde transport and macropinocytosis. Itai N, et al. PLoS One, 2018. PMID 30419003, Free PMC Article
  4. Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virion and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication. Schuchman R, et al. J Virol, 2018 Jul 15. PMID 29743363, Free PMC Article
  5. Structural basis for the hijacking of endosomal sorting nexin proteins by Chlamydia trachomatis. Paul B, et al. Elife, 2017 Feb 22. PMID 28226239, Free PMC Article

See all (87) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SNX5 promotes antigen presentation in B cells by dual regulation of actin and lysosomal dynamics.
    Title: SNX5 promotes antigen presentation in B cells by dual regulation of actin and lysosomal dynamics.
  2. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
    Title: The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
  3. Overexpression of lncRNA HOXA-AS2 promotes the progression of oral squamous cell carcinoma by mediating SNX5 expression.
    Title: Overexpression of lncRNA HOXA-AS2 promotes the progression of oral squamous cell carcinoma by mediating SNX5 expression.
  4. Sorting nexin 5 mediates virus-induced autophagy and immunity.
    Title: Sorting nexin 5 mediates virus-induced autophagy and immunity.
  5. Upregulation of SNX5 predicts poor prognosis and promotes hepatocellular carcinoma progression by modulating the EGFR-ERK1/2 signaling pathway.
    Title: Upregulation of SNX5 predicts poor prognosis and promotes hepatocellular carcinoma progression by modulating the EGFR-ERK1/2 signaling pathway.
  6. SNX5 inhibits RLR-mediated antiviral signaling by targeting RIG-I-VISA signalosome.
    Title: SNX5 inhibits RLR-mediated antiviral signaling by targeting RIG-I-VISA signalosome.
  7. The studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the 'Endosomal SNX-BAR sorting complex for promoting exit 1' (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers.
    Title: Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins.
  8. Results indicate that SNX5 constitutive phosphorylation that mimics the mutant S226E decreases the active SNX5 in these cells. The phosphorylation of SNX5 regulates the dimerization with SNX1 or SNX2, and this suggests that it controls membrane trafficking and protein sorting.
    Title: The phosphorylation of sorting nexin 5 at serine 226 regulates retrograde transport and macropinocytosis.
  9. High SNX5 expression is associated with alphavirus infections.
    Title: Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virion and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication.
  10. sorting nexin 5 (SNX5), a component of the retromer and part of the retrograde transport pathway, interacts with UL35 proteins. binding of UL35 proteins to SNX5 was required for efficient viral replication and for transport of the most abundant cytomegalovirus glycoprotein B to the cytoplasmic viral assembly center.
    Title: Interaction of Human Cytomegalovirus Tegument Proteins ppUL35 and ppUL35A with Sorting Nexin 5 Regulates Glycoprotein B (gpUL55) Localization.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

Go to the top of the page Help

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
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ10931

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables D1 dopamine receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables cadherin binding HDA PubMed 
enables dynactin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables dynactin 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 phosphatidylinositol binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol-3,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-4-phosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-5-phosphate 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 epidermal growth factor catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of blood pressure IEA
Inferred from Electronic Annotation
more info
  
involved_in pinocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pinocytosis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of insulin receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in brush border IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic side of early endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in macropinocytic cup IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in phagocytic cup IEA
Inferred from Electronic Annotation
more info
  
part_of retromer complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of retromer, tubulation complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in ruffle IEA
Inferred from Electronic Annotation
more info
  
located_in tubular endosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
sorting nexin-5

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001282454.2 → NP_001269383.1  sorting nexin-5 isoform b

    See identical proteins and their annotated locations for NP_001269383.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' structure, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    BC000100, BC062638, DA567854
    UniProtKB/TrEMBL
    Q6P5V6
    Related
    ENST00000490175.5
    Conserved Domains (2) summary
    cd07663
    Location:80 → 297
    BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5
    cl02563
    Location:1 → 64
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  2. NM_014426.4 → NP_055241.1  sorting nexin-5 isoform a

    See identical proteins and their annotated locations for NP_055241.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript. Variants 1 and 2 encode the same protein (isoform a).
    Source sequence(s)
    BC000100, BC093623, DB118420
    Consensus CDS
    CCDS13130.1
    UniProtKB/Swiss-Prot
    B7ZKN3, D3DW26, Q52LC4, Q7KZN0, Q9BWP0, Q9Y5X3
    UniProtKB/TrEMBL
    Q53FH8
    Related
    ENSP00000366988.3, ENST00000377759.9
    Conserved Domains (2) summary
    cd07291
    Location:29 → 169
    PX_SNX5; The phosphoinositide binding Phox Homology domain of Sorting Nexin 5
    cd07663
    Location:185 → 402
    BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5

  3. NM_152227.3 → NP_689413.1  sorting nexin-5 isoform a

    See identical proteins and their annotated locations for NP_689413.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 2. Variants 1 and 2 encode the same protein (isoform a).
    Source sequence(s)
    AF121855, BC000100
    Consensus CDS
    CCDS13130.1
    UniProtKB/Swiss-Prot
    B7ZKN3, D3DW26, Q52LC4, Q7KZN0, Q9BWP0, Q9Y5X3
    UniProtKB/TrEMBL
    Q53FH8
    Related
    ENSP00000366998.3, ENST00000377768.7
    Conserved Domains (2) summary
    cd07291
    Location:29 → 169
    PX_SNX5; The phosphoinositide binding Phox Homology domain of Sorting Nexin 5
    cd07663
    Location:185 → 402
    BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    17941600..17968794 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    17992739..18019917 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5X3.1 GenPept UniProtKB/Swiss-Prot:Q9Y5X3

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous