SNX4 sorting nexin 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX4provided by HGNC
Official Full Name: sorting nexin 4provided by HGNC
Primary source: HGNC:HGNC:11175
See related: Ensembl:ENSG00000114520 MIM:605931; AllianceGenome:HGNC:11175
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: ATG24B
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 associated with the long isoform of the leptin receptor and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor in cell cultures, but its function is unknown. This protein may form oligomeric complexes with family members. Two transcript variants, one protein coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Nov 2012]
Expression: Ubiquitous expression in thyroid (RPKM 29.2), kidney (RPKM 26.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q21.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (125446650..125520202, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (128173305..128246821, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (125165494..125239046, complement)

Chromosome 3 - NC_000003.12 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 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?

The phosphatidylinositol 3-phosphate-binding protein SNX4 controls ATG9A recycling and autophagy.
Title: The phosphatidylinositol 3-phosphate-binding protein SNX4 controls ATG9A recycling and autophagy.
Results indicate that SNX4-mediated regulation of the steady-state levels and trafficking of BACE1, as well as the subsequent increase in BACE1-mediated cleavage, may be relevant to Alzheimer's disease progression.
Title: Sorting nexin-4 regulates β-amyloid production by modulating β-site-activating cleavage enzyme-1.
alpha-taxilin interacts with SNX4 and plays a role in the recycling pathway of TfnR.
Title: α-Taxilin interacts with sorting nexin 4 and participates in the recycling pathway of transferrin receptor.
SNX4, but not SNX1 and SNX8, is associated with the Rab11-recycling endosomes and that a high frequency of SNX4-mediated tubule formation is observed as endosomes undergo Rab4-to-Rab11 transition.
Title: SNX-BAR-mediated endosome tubulation is co-ordinated with endosome maturation.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
clathrin serving as a regulator of SNX4-dependent transport; upon clathrin release, dynein may bind SNX4 and mediate retrograde movement
Title: SNX4 in complex with clathrin and dynein: implications for endosome movement.
by driving membrane tubulation, SNX4 coordinates iterative, geometric-based sorting of the TfnR with the long-range transport of carriers from early endosomes to the ERC
Title: SNX4 coordinates endosomal sorting of TfnR with dynein-mediated transport into the endocytic recycling compartment.
study indicates that hVps34 and its product PI(3)P are involved in endosome to Golgi transport of ricin, and that SNX2 and SNX4 are likely to be effectors in this pathway
Title: Phosphoinositide-regulated retrograde transport of ricin: crosstalk between hVps34 and sorting nexins.
Sorting nexin 4 and amphiphysin 2 have roles in endocytosis and intracellular trafficking
Title: Sorting nexin 4 and amphiphysin 2, a new partnership between endocytosis and intracellular trafficking.

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Phenotypes

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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

D3S4226 (e-PCR)
- UniSTS:59784

RH103376 (e-PCR)
- UniSTS:97703

SHGC-77294 (e-PCR)
- UniSTS:5296

SNX4 (e-PCR)
- UniSTS:505539

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables epidermal growth factor receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables insulin receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables leptin receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphatidylinositol-3-phosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3-phosphate binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferrin receptor binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of histamine secretion by mast cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of cytoplasmic dynein complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in early endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in early endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay 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 presynaptic endosome	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sorting nexin-4

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_003794.4 → NP_003785.1 sorting nexin-4

See identical proteins and their annotated locations for NP_003785.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and is the protein-coding variant.

Source sequence(s)

AI187416, AK001835, DA289870

Consensus CDS

CCDS3032.1

UniProtKB/Swiss-Prot

B3KMH0, B4DQV4, D3DNA3, O95219

Related

ENSP00000251775.4, ENST00000251775.9

Conserved Domains (2) summary

cd06864
Location:58 → 184

PX_SNX4; The phosphoinositide binding Phox Homology domain of Sorting Nexin 4

cd07622
Location:205 → 448

BAR_SNX4; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4

RNA

NR_073435.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI187416, AK001835, AK298972, DA289870