SNX5 sorting nexin 5 [Homo sapiens (human)] - Gene

Summary

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
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Genomic context

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Sorting nexin 5 mediates virus-induced autophagy and immunity.
Title: Sorting nexin 5 mediates virus-induced autophagy and immunity.
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.
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.
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.
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.
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.
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

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL035224 (e-PCR)
- UniSTS:94722

D11S2921 (e-PCR)
- UniSTS:152074

D20S550E (e-PCR)
- UniSTS:86294

G20280 (e-PCR)
- UniSTS:26927

PMC156606P1 (e-PCR)
- UniSTS:271408

A005K08 (e-PCR)
- UniSTS:26928

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

L18426 (e-PCR)
- UniSTS:34648

RH94213 (e-PCR)
- UniSTS:85341

NoName (e-PCR)
- UniSTS:483189

D11S3114 (e-PCR)
- UniSTS:152207

AA851347 (e-PCR)
- UniSTS:243367

RH36045 (e-PCR)
- UniSTS:53455

SHGC-64282 (e-PCR)
- UniSTS:52956

RH38955 (e-PCR)
- UniSTS:83935

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 more info	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

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Preferred Names: sorting nexin-5

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)

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
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
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