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Aliases for SNX3 Gene

Aliases for SNX3 Gene

  • Sorting Nexin 3 2 3 5
  • Sorting Nexin 3A 3
  • Sorting Nexin-3 3
  • Protein SDP3 4
  • MCOPS8 3
  • Grd19 3
  • SDP3 3

External Ids for SNX3 Gene

Previous GeneCards Identifiers for SNX3 Gene

  • GC06M108382
  • GC06M108555
  • GC06M108578
  • GC06M108639
  • GC06M106100

Summaries for SNX3 Gene

Entrez Gene Summary for SNX3 Gene

  • 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 most family members. This protein interacts with phosphatidylinositol-3-phosphate, and is involved in protein trafficking. A pseudogene of this gene is present on the sex chromosomes. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

GeneCards Summary for SNX3 Gene

SNX3 (Sorting Nexin 3) is a Protein Coding gene. Diseases associated with SNX3 include Microphthalmia, Syndromic 8 and Robinow Syndrome, Autosomal Dominant 2. Among its related pathways are Deubiquitination and Signaling by GPCR. GO annotations related to this gene include phosphatidylinositol binding and phosphatidylinositol-3-phosphate binding. An important paralog of this gene is SNX12.

UniProtKB/Swiss-Prot for SNX3 Gene

  • Phosphoinositide-binding protein required for multivesicular body formation. Specifically binds phosphatidylinositol 3-phosphate (PtdIns(P3)). Also can bind phosphatidylinositol 4-phosphate (PtdIns(P4)), phosphatidylinositol 5-phosphate (PtdIns(P5)) and phosphatidylinositol 3,5-biphosphate (PtdIns(3,5)P2) (By similarity). Plays a role in protein transport between cellular compartments. Together with RAB7A facilitates endosome membrane association of the retromer cargo-selective subcomplex (CSC/VPS). May in part act as component of the SNX3-retromer complex which mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway (PubMed:21725319, PubMed:24344282). Promotes stability and cell surface expression of epithelial sodium channel (ENAC) subunits SCNN1A and SCNN1G (By similarity). Not involved in EGFR degradation. Involved in the regulation of phagocytosis in dendritic cells possibly by regulating EEA1 recruitment to the nascent phagosomes (PubMed:23237080). Involved in iron homeostasis through regulation of endocytic recycling of the transferrin receptor TFRC presumably by delivering the tranferrin:transferrin receptor complex to recycling endosomes; the function may involve the CSC retromer subcomplex (By similarity). In the case of Salmonella enterica infection plays arole in maturation of the Salmonella-containing vacuole (SCV) and promotes recruitment of LAMP1 to SCVs (PubMed:20482551).

Gene Wiki entry for SNX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNX3 Gene

Genomics for SNX3 Gene

Regulatory Elements for SNX3 Gene

Enhancers for SNX3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G108293 1.2 ENCODE 12.4 -33.9 -33858 2.4 CREB3L1 DMAP1 YY1 ZNF143 SP3 TBX21 ZNF610 GLIS1 NBN NR2C1 SNX3 AFG1L RPL36AP24
GH06G108301 1 ENCODE dbSUPER 12.4 -41.1 -41077 2.3 ZNF263 CTCF BHLHE40 MAX RAD21 YY1 FOSL1 JUND ATF3 HNF4G SNX3 OSTM1 NR2E1 SEC63 AFG1L RPL36AP24
GH06G108360 1 ENCODE 10.9 -100.2 -100233 1.5 PKNOX1 ATF1 ARNT TCF12 ZNF766 ELK1 GATA2 ZMIZ1 NCOA1 REST SNX3 OSTM1 NR2E1 LOC100506224 ENSG00000238055
GH06G108311 0.9 ENCODE dbSUPER 10.8 -51.7 -51650 2.0 GATAD2A FOXA2 RFX1 ZNF384 RARA FOXA1 TBX3 RFX3 HNF4A FOXJ2 SNX3 OSTM1 NR2E1 RPL36AP24 AFG1L
GH06G108298 0.7 dbSUPER 12.4 -38.4 -38383 2.4 CTCF ZIC2 ZNF335 ZBTB48 ZSCAN5C SMC3 ZNF600 FOS IKZF2 MTA2 SNX3 AFG1L RPL36AP24
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNX3 on UCSC Golden Path with GeneCards custom track

Promoters for SNX3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000200801 460 2801 HDGF PKNOX1 MLX CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 YY1

Genomic Location for SNX3 Gene

Chromosome:
6
Start:
108,211,217 bp from pter
End:
108,261,260 bp from pter
Size:
50,044 bases
Orientation:
Minus strand

Genomic View for SNX3 Gene

Genes around SNX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNX3 Gene

Proteins for SNX3 Gene

  • Protein details for SNX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60493-SNX3_HUMAN
    Recommended name:
    Sorting nexin-3
    Protein Accession:
    O60493
    Secondary Accessions:
    • A8K0B1
    • E1P5E4
    • E1P5E5
    • O60718
    • Q4TT29
    • Q4TT31
    • Q5JXJ7
    • Q5JXJ8
    • Q96AP9
    • Q9C0J5
    • Q9NU45

    Protein attributes for SNX3 Gene

    Size:
    162 amino acids
    Molecular mass:
    18762 Da
    Quaternary structure:
    • Interacts with VPS26A, VPS29 and VPS35; the interaction with VPS35 is direct. The association with the retromer CSC subcomplex subunits is proposed to represent a functional distinct retromer variant described as SNX3-retromer complex (PubMed:21725319, PubMed:24344282). Interacts with USP10 and SCNN1A (By similarity). Interacts with TRFC (By similarity). Interacts with SNX8; 2 molecules of SNX8 seems to associate with one molecule of SNX3 (PubMed:24866125). Interacts with PTPRU (PubMed:17622474).

    Three dimensional structures from OCA and Proteopedia for SNX3 Gene

    Alternative splice isoforms for SNX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNX3 Gene

Post-translational modifications for SNX3 Gene

  • Ubiquitinated, leading to its proteasomal degradation. Deubiquitinated by USP10 (By similarity).
  • Ubiquitination at Lys95, isoforms=2, 4119, and isoforms=2, 4128
  • Modification sites at PhosphoSitePlus

Other Protein References for SNX3 Gene

No data available for DME Specific Peptides for SNX3 Gene

Domains & Families for SNX3 Gene

Gene Families for SNX3 Gene

Protein Domains for SNX3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SNX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O60493

UniProtKB/Swiss-Prot:

SNX3_HUMAN :
  • The PX domain mediates specific binding to phosphatidylinositol 3-phosphate (PtdIns(P3)).
  • Belongs to the sorting nexin family.
Domain:
  • The PX domain mediates specific binding to phosphatidylinositol 3-phosphate (PtdIns(P3)).
Family:
  • Belongs to the sorting nexin family.
genes like me logo Genes that share domains with SNX3: view

Function for SNX3 Gene

Molecular function for SNX3 Gene

UniProtKB/Swiss-Prot Function:
Phosphoinositide-binding protein required for multivesicular body formation. Specifically binds phosphatidylinositol 3-phosphate (PtdIns(P3)). Also can bind phosphatidylinositol 4-phosphate (PtdIns(P4)), phosphatidylinositol 5-phosphate (PtdIns(P5)) and phosphatidylinositol 3,5-biphosphate (PtdIns(3,5)P2) (By similarity). Plays a role in protein transport between cellular compartments. Together with RAB7A facilitates endosome membrane association of the retromer cargo-selective subcomplex (CSC/VPS). May in part act as component of the SNX3-retromer complex which mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway (PubMed:21725319, PubMed:24344282). Promotes stability and cell surface expression of epithelial sodium channel (ENAC) subunits SCNN1A and SCNN1G (By similarity). Not involved in EGFR degradation. Involved in the regulation of phagocytosis in dendritic cells possibly by regulating EEA1 recruitment to the nascent phagosomes (PubMed:23237080). Involved in iron homeostasis through regulation of endocytic recycling of the transferrin receptor TFRC presumably by delivering the tranferrin:transferrin receptor complex to recycling endosomes; the function may involve the CSC retromer subcomplex (By similarity). In the case of Salmonella enterica infection plays arole in maturation of the Salmonella-containing vacuole (SCV) and promotes recruitment of LAMP1 to SCVs (PubMed:20482551).

Gene Ontology (GO) - Molecular Function for SNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17474147
GO:0008289 lipid binding IEA --
GO:0010314 phosphatidylinositol-5-phosphate binding ISS --
GO:0019903 protein phosphatase binding IPI 17622474
GO:0032266 phosphatidylinositol-3-phosphate binding IDA 11433298
genes like me logo Genes that share ontologies with SNX3: view
genes like me logo Genes that share phenotypes with SNX3: view

Animal Models for SNX3 Gene

MGI Knock Outs for SNX3:
  • Snx3 tm1.1(KOMP)Vlcg

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SNX3 Gene

Localization for SNX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNX3 Gene

Early endosome. Cytoplasmic vesicle, phagosome. Note=Colocalizes to clathrin-coated endosomal vesicles morphologically distinct from retromer-decorated non-branched endosomal tubule structures (PubMed:21725319) Colocalizes with EEA1 on nascent phagosomes in dendritic cells but competes with EEA1 for binding to phagosomal membrane (PubMed:23237080). In the case of Salmonella enterica infection localizes to Salmonella-containing vacuoles (SCVs) from which SNX3-containing tubules form 30-60 min after infection (PubMed:20482551). {ECO:0000269 PubMed:20482551, ECO:0000269 PubMed:21725319, ECO:0000269 PubMed:23237080}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SNX3 gene
Compartment Confidence
extracellular 5
cytosol 5
endosome 5
nucleus 2
golgi apparatus 2
plasma membrane 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 11279102
GO:0005768 endosome IEA --
GO:0005769 early endosome IDA,IEA 11433298
GO:0005829 cytosol TAS --
GO:0010008 endosome membrane TAS --
genes like me logo Genes that share ontologies with SNX3: view

Pathways & Interactions for SNX3 Gene

genes like me logo Genes that share pathways with SNX3: view

Pathways by source for SNX3 Gene

Gene Ontology (GO) - Biological Process for SNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0009617 response to bacterium IDA 20482551
GO:0010324 membrane invagination IDA 18767904
GO:0010976 positive regulation of neuron projection development ISS --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with SNX3: view

No data available for SIGNOR curated interactions for SNX3 Gene

Drugs & Compounds for SNX3 Gene

(1) Drugs for SNX3 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S,S-(2-Hydroxyethyl)Thiocysteine Experimental Pharma Target 0
genes like me logo Genes that share compounds with SNX3: view

Transcripts for SNX3 Gene

Unigene Clusters for SNX3 Gene

Sorting nexin 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SNX3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e
SP1: -
SP2: -
SP3: - - -
SP4: - -
SP5: - - -
SP6: - - -

Relevant External Links for SNX3 Gene

GeneLoc Exon Structure for
SNX3
ECgene alternative splicing isoforms for
SNX3

Expression for SNX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SNX3 Gene



Protein tissue co-expression partners for SNX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SNX3 Gene:

SNX3

SOURCE GeneReport for Unigene cluster for SNX3 Gene:

Hs.12102

Evidence on tissue expression from TISSUES for SNX3 Gene

  • Nervous system(4.9)
  • Pancreas(4.5)
  • Skin(4.5)
  • Intestine(4.4)
  • Liver(4.4)
  • Blood(4.1)
  • Lung(2.9)
  • Adrenal gland(2.1)
  • Bone marrow(2.1)
  • Heart(2.1)
  • Lymph node(2.1)
  • Muscle(2.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with SNX3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNX3 Gene

Orthologs for SNX3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SNX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNX3 34 35
  • 99.59 (n)
oppossum
(Monodelphis domestica)
Mammalia SNX3 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SNX3 34 35
  • 94.44 (n)
cow
(Bos Taurus)
Mammalia SNX3 34 35
  • 93.83 (n)
mouse
(Mus musculus)
Mammalia Snx3 34 16 35
  • 93.42 (n)
rat
(Rattus norvegicus)
Mammalia Snx3 34
  • 92.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SNX3 35
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves SNX3 34 35
  • 83.33 (n)
lizard
(Anolis carolinensis)
Reptilia SNX3 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snx3 34
  • 80.86 (n)
MGC75986 34
African clawed frog
(Xenopus laevis)
Amphibia MGC68580 34
zebrafish
(Danio rerio)
Actinopterygii snx3 34 35
  • 74.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6359 36
  • 70 (a)
Snx3 35
  • 68 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea snx-3 35
  • 67 (a)
OneToMany
W06D4.5 36
  • 66 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SNX3 34 35
  • 53.55 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR390C 34
  • 49.11 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A03718g 34
  • 49.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 66 (a)
OneToMany
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes snx3 34
  • 52.85 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01914 34
  • 52.53 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4323 34
Species where no ortholog for SNX3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SNX3 Gene

ENSEMBL:
Gene Tree for SNX3 (if available)
TreeFam:
Gene Tree for SNX3 (if available)

Paralogs for SNX3 Gene

Paralogs for SNX3 Gene

(6) SIMAP similar genes for SNX3 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for SNX3 Gene

genes like me logo Genes that share paralogs with SNX3: view

Variants for SNX3 Gene

Sequence variations from dbSNP and Humsavar for SNX3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000034486 -- 108,229,665(+) GGCCT(A/C)AGCCA intron-variant
rs1000083241 -- 108,218,419(+) CACAT(C/T)GCTGG intron-variant
rs1000099889 -- 108,224,247(+) TGCAG(C/G)GTCAT intron-variant
rs1000111234 -- 108,212,494(+) CATCA(A/T)GCCCA intron-variant
rs1000134691 -- 108,246,306(+) GCTTT(A/C/G)AGCAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SNX3 Gene

Variant ID Type Subtype PubMed ID
esv2657747 CNV deletion 23128226
esv3610314 CNV loss 21293372
nsv830766 CNV loss 17160897

Variation tolerance for SNX3 Gene

Residual Variation Intolerance Score: 34.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.10; 2.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SNX3 Gene

Human Gene Mutation Database (HGMD)
SNX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNX3 Gene

Disorders for SNX3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SNX3 Gene - From: OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 8
  • microphthalmia syndromic 8
robinow syndrome, autosomal dominant 2
  • autosomal dominant robinow syndrome 2
microphthalmia
  • microphthalmos
- elite association - COSMIC cancer census association via MalaCards
Search SNX3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SNX3_HUMAN
  • Microphthalmia, syndromic, 8 (MCOPS8) [MIM:601349]: A very rare congenital syndrome characterized by microcephaly, microphthalmia, ectrodactyly of the lower limbs and prognathism. Intellectual deficit has been reported. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269 PubMed:12471201}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving SNX3 has been found in patients with syndromic microphthalmia. Translocation t(6;13)(q21;q12).

Relevant External Links for SNX3

Genetic Association Database (GAD)
SNX3
Human Genome Epidemiology (HuGE) Navigator
SNX3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNX3
genes like me logo Genes that share disorders with SNX3: view

No data available for Genatlas for SNX3 Gene

Publications for SNX3 Gene

  1. Identification of a family of sorting nexin molecules and characterization of their association with receptors. (PMID: 9819414) Haft C.R. … Taylor S.I. (Mol. Cell. Biol. 1998) 2 3 4 22 64
  2. Sorting nexin 3 (SNX3) is disrupted in a patient with a translocation t(6;13)(q21;q12) and microcephaly, microphthalmia, ectrodactyly, prognathism (MMEP) phenotype. (PMID: 12471201) Vervoort V.S. … Schwartz C.E. (J. Med. Genet. 2002) 3 4 22 64
  3. A mechanism for retromer endosomal coat complex assembly with cargo. (PMID: 24344282) Harrison M.S. … Burd C.G. (Proc. Natl. Acad. Sci. U.S.A. 2014) 3 4 64
  4. SNX3 recruits to phagosomes and negatively regulates phagocytosis in dendritic cells. (PMID: 23237080) Chua R.Y. … Wong S.H. (Immunology 2013) 3 4 64
  5. A SNX3-dependent retromer pathway mediates retrograde transport of the Wnt sorting receptor Wntless and is required for Wnt secretion. (PMID: 21725319) Harterink M. … Korswagen H.C. (Nat. Cell Biol. 2011) 3 4 64

Products for SNX3 Gene

Sources for SNX3 Gene

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