SNX9 sorting nexin 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX9provided by HGNC
Official Full Name: sorting nexin 9provided by HGNC
Primary source: HGNC:HGNC:14973
See related: Ensembl:ENSG00000130340 MIM:605952; AllianceGenome:HGNC:14973
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: SDP1; WISP; SH3PX1; SH3PXD3A
Summary: This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in gall bladder (RPKM 27.0), esophagus (RPKM 26.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q25.3

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (157823246..157945077)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (159069178..159191298)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (158244278..158366109)

Chromosome 6 - NC_000006.12 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
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?

Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy.
Title: Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy.
SNX9-induced membrane tubulation regulates CD28 cluster stability and signalling.
Title: SNX9-induced membrane tubulation regulates CD28 cluster stability and signalling.
SNX9 depletion significantly delayed the recycling of integrin beta1
Title: SNX9 determines the surface levels of integrin β1 in vascular endothelial cells: Implication in poor prognosis of human colorectal cancers overexpressing SNX9.
NECAP recruits drivers of late stages of clathrin-coated pit (CCP) formation, including SNX9, via a site distinct from where NECAP binds AP2.
Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.
SNX9 knockdown revealed a nonredundant effect on overall ADAM9 protein levels, resulting in increased ADAM9 levels at the cell surface
Title: Sorting nexin 9 (SNX9) regulates levels of the transmembrane ADAM9 at the cell surface.
SNX9 assembles into ring-like structures around the endocytic vesicles
Title: Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission.
In conclusion, the authors identified SNX9 as a facilitator of podocin endocytosis in severe podocyte injury and demonstrated the expression of SNX9 in the podocytes of both nephropathy model mice and human patients with irreversible glomerular disease.
Title: Sorting Nexin 9 facilitates podocin endocytosis in the injured podocyte.
The diversified changes associated with SNX9 expression in cancer highlight its importance as a central regulator of cancer cell behavior.
Title: Sorting nexin 9 negatively regulates invadopodia formation and function in cancer cells.
reduced levels of SNX9 were observed in blood samples from colorectal cancer patients, emphasizing the feasibility of its use as a diagnostic and prognostic biomarker sensing the host's immune status and inflammatory stage.
Title: Impaired SNX9 Expression in Immune Cells during Chronic Inflammation: Prognostic and Diagnostic Implications.
this study shows that SNX9 uses a unique mechanism to induce the tubulation of the plasma membrane which mediates proper membrane deformation during clathrin-mediated endocytosis.
Title: The unique mechanism of SNX9 BAR domain for inducing membrane tubulation.

Submit: New GeneRIF Correction See all GeneRIFs (32)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18342 (e-PCR)
- UniSTS:39684

WI-19319 (e-PCR)
- UniSTS:69893

D11S2921 (e-PCR)
- UniSTS:152074

RH92174 (e-PCR)
- UniSTS:87871

L18426 (e-PCR)
- UniSTS:34648

D12S1332 (e-PCR)
- UniSTS:48481

RH15827 (e-PCR)
- UniSTS:16759

STS-AA010032 (e-PCR)
- UniSTS:80548

RH26809 (e-PCR)
- UniSTS:88261

SHGC-132189 (e-PCR)
- UniSTS:170699

STS-R69163 (e-PCR)
- UniSTS:61429

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 1-phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
enables Arp2/3 complex binding	IDA Inferred from Direct Assay more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction 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 protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase 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	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 intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid tube assembly	IDA Inferred from Direct Assay 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 plasma membrane tubulation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of GTPase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of actin filament polymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of membrane protein ectodomain proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in clathrin-coated pit	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cuticular plate	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	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 cytoplasmic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IEA Inferred from Electronic Annotation more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sorting nexin-9

Names: SH3 and PX domain-containing protein 1; SH3 and PX domain-containing protein 3A; Wiskott-Aldrich syndrome protein (WASP) interactor 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.

mRNA and Protein(s)

NM_016224.5 → NP_057308.1 sorting nexin-9

See identical proteins and their annotated locations for NP_057308.1

Status: REVIEWED

Source sequence(s)

AF121859, AL139330, DA336311

Consensus CDS

CCDS5253.1

UniProtKB/Swiss-Prot

Q9BSI7, Q9BVM1, Q9UJH6, Q9UP20, Q9Y5X1

UniProtKB/TrEMBL

B2RAU5

Related

ENSP00000376024.3, ENST00000392185.8

Conserved Domains (3) summary

cd07285
Location:250 → 375

PX_SNX9; The phosphoinositide binding Phox Homology domain of Sorting Nexin 9

cd07668
Location:386 → 595

BAR_SNX9; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9

cd11898
Location:4 → 60

SH3_SNX9; Src Homology 3 domain of Sorting nexin 9

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

157823246..157945077

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011535886.4 → XP_011534188.1 sorting nexin-9 isoform X1

UniProtKB/TrEMBL

A0A7P0T8Z7

Conserved Domains (2) summary

cd07285
Location:156 → 281

PX_SNX9; The phosphoinositide binding Phox Homology domain of Sorting Nexin 9

cd07668
Location:292 → 501

BAR_SNX9; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9