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Aliases for SNX6 Gene

Aliases for SNX6 Gene

  • Sorting Nexin 6 2 3 5
  • TRAF4-Associated Factor 2 3 4
  • Tumor Necrosis Factor Receptor-Associated Factor 4(TRAF4)-Associated Factor 2 3
  • Sorting Nexin-6 3
  • MSTP010 3
  • TFAF2 3

External Ids for SNX6 Gene

Previous GeneCards Identifiers for SNX6 Gene

  • GC14M032408
  • GC14M028818
  • GC14M033020
  • GC14M034100
  • GC14M035030
  • GC14M015145

Summaries for SNX6 Gene

Entrez Gene Summary for SNX6 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 associates with the long isoform of the leptin receptor, the transforming growth factor-beta family of receptor serine-threonine kinases, and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor. This protein may form oligomeric complexes with family member proteins through interactions of both the PX domain and the coiled coil regions of the molecules. Translocation of this protein from the cytoplasm to the nucleus occurs after binding to proviral integration site 1 protein. This gene results in two transcripts encoding two distinct isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for SNX6 Gene

SNX6 (Sorting Nexin 6) is a Protein Coding gene. Among its related pathways are SMAD Signaling Network and Endocytosis. GO annotations related to this gene include protein homodimerization activity and type I transforming growth factor beta receptor binding. An important paralog of this gene is SNX32.

UniProtKB/Swiss-Prot for SNX6 Gene

  • Involved in several stages of intracellular trafficking. Interacts with membranes phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate (Probable). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex (PubMed:19935774). The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptor IGF2R (PubMed:17148574). May function as link between transport vesicles and dynactin (Probable). Negatively regulates retrograde transport of BACE1 from the cell surface to the trans-Golgi network (PubMed:20354142). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). In association with GIT1 involved in EGFR degradation. Promotes lysosomal degradation of CDKN1B (By similarity). May contribute to transcription regulation (Probable).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNX6 Gene

Genomics for SNX6 Gene

Regulatory Elements for SNX6 Gene

Enhancers for SNX6 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
GH14G034578 0.9 dbSUPER 19.7 +49.6 49633 3.2 FOXA2 PKNOX1 ARNT ARID4B ZNF48 YY1 ZNF121 MXD4 ZNF592 NFIL3 SNX6 RNU1-27P EAPP SPTSSA RPS19P3
GH14G034604 0.7 Ensembl ENCODE 21.7 +24.8 24783 1.2 GATA3 ZNF384 SNX6 RNU1-27P EAPP CFL2 RPS19P3
GH14G034855 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10.6 -227.0 -227005 2.5 FOXA2 FUS CEBPB ATF2 FOXA1 SNX6 FAM177A1 RPL23AP8 BAZ1A KIAA0391 RALGAPA1 PPP2R3C PSMA6 RNU7-41P ENSG00000258738
GH14G034536 1.4 ENCODE dbSUPER 9.1 +91.4 91449 4.1 HNRNPUL1 HDGF PKNOX1 FOXA2 MLX ZFP64 WRNIP1 ARID4B SIN3A DMAP1 SNX6 EAPP RPL23AP71
GH14G034495 1.3 Ensembl ENCODE 7.7 +132.7 132712 3.5 PKNOX1 FOXA2 MLX ZFP64 ARID4B SLC30A9 ZNF766 ZNF143 FOS DEK SNX6 SPTSSA KIAA0391 RPL23AP71 EAPP
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNX6 on UCSC Golden Path with GeneCards custom track

Promoters for SNX6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000067576 383 2000 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF48 GLIS2 ZNF207 KLF7 ZNF263

Genomic Location for SNX6 Gene

Chromosome:
14
Start:
34,561,094 bp from pter
End:
34,630,183 bp from pter
Size:
69,090 bases
Orientation:
Minus strand

Genomic View for SNX6 Gene

Genes around SNX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNX6 Gene

Proteins for SNX6 Gene

  • Protein details for SNX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UNH7-SNX6_HUMAN
    Recommended name:
    Sorting nexin-6
    Protein Accession:
    Q9UNH7
    Secondary Accessions:
    • C0H5W9
    • Q9Y449

    Protein attributes for SNX6 Gene

    Size:
    406 amino acids
    Molecular mass:
    46649 Da
    Quaternary structure:
    • Forms heterodimers with BAR domain-containing sorting nexins SNX1 and SNX2 (PubMed:23085988). The heterodimers are proposed to self-assemble into helical arrays on the membrane to stabilize and expand local membrane curvature underlying endosomal tubule formation. Thought to be a component of the originally described retromer complex (also called SNX-BAR retromer) which is a pentamer containing the heterotrimeric retromer cargo-selective complex (CSC), also descibed as vacuolar protein sorting subcomplex (VPS), and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity (Probable). Interacts with SNX1, SNX2, VPS26A, VPS29, VPS35, CDKN1B, TGFB receptors, BACE1, BRMS1, PIP5K1C isoform 3. Interacts with DCTN1; the association with DCTN1 is involved in movement of retromer-c ontaining vesicles toward the TGN (PubMed:11279102, PubMed:17148574, PubMed:19935774, PubMed:19619496, PubMed:20354142, PubMed:20830743, PubMed:23085988, PubMed:24610942). Interacts with CDKN1B and GIT1 (By similarity). Interacts with PIM1; translocating SNX6 to the nucleus (PubMed:11591366).
    SequenceCaution:
    • Sequence=AAD24202.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SNX6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNX6 Gene

Post-translational modifications for SNX6 Gene

  • In vitro phosphorylated by PIM1; not affecting PIM1-dependent nuclear translocation (PubMed:11591366).
  • Ubiquitination at isoforms=60, isoforms=119, Lys189, isoforms=2204, isoforms=2265, isoforms=2291, and Lys375
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SNX6 Gene

Domains & Families for SNX6 Gene

Gene Families for SNX6 Gene

Protein Domains for SNX6 Gene

Suggested Antigen Peptide Sequences for SNX6 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UNH7

UniProtKB/Swiss-Prot:

SNX6_HUMAN :
  • The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate.
  • Belongs to the sorting nexin family.
Domain:
  • The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate.
  • The BAR domain is able to sense membrane curvature upon dimerization. Membrane remodeling seems to implicate insertion of an amphipatric helix (AH) in the membrane (Probable).
Family:
  • Belongs to the sorting nexin family.
genes like me logo Genes that share domains with SNX6: view

Function for SNX6 Gene

Molecular function for SNX6 Gene

UniProtKB/Swiss-Prot Function:
Involved in several stages of intracellular trafficking. Interacts with membranes phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate (Probable). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex (PubMed:19935774). The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptor IGF2R (PubMed:17148574). May function as link between transport vesicles and dynactin (Probable). Negatively regulates retrograde transport of BACE1 from the cell surface to the trans-Golgi network (PubMed:20354142). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). In association with GIT1 involved in EGFR degradation. Promotes lysosomal degradation of CDKN1B (By similarity). May contribute to transcription regulation (Probable).

Gene Ontology (GO) - Molecular Function for SNX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11278302
GO:0008289 lipid binding IEA --
GO:0034452 dynactin binding IDA 19619496
GO:0034713 type I transforming growth factor beta receptor binding IEA --
GO:0035091 phosphatidylinositol binding IBA,IEA --
genes like me logo Genes that share ontologies with SNX6: view
genes like me logo Genes that share phenotypes with SNX6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNX6 Gene

Localization for SNX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNX6 Gene

Early endosome. Early endosome membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasmic vesicle. Cytoplasm. Nucleus. Note=Interaction with SNX1 or SNX2 promotes location at endosome membranes (PubMed:19935774). Only a minor proportion is seen in the nucleus. {ECO:0000269 PubMed:19935774}.

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 SNX6 gene
Compartment Confidence
endosome 5
nucleus 4
cytosol 4
golgi apparatus 2
lysosome 1

Gene Ontology (GO) - Cellular Components for SNX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular NAS,IEA 11279102
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IDA,IEA 11279102
GO:0005764 lysosome IDA --
GO:0005768 endosome IDA --
genes like me logo Genes that share ontologies with SNX6: view

Pathways & Interactions for SNX6 Gene

genes like me logo Genes that share pathways with SNX6: view

Pathways by source for SNX6 Gene

1 KEGG pathway for SNX6 Gene
1 Qiagen pathway for SNX6 Gene

Gene Ontology (GO) - Biological Process for SNX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport NAS,IEA 11279102
GO:0006897 endocytosis IBA --
GO:0007175 negative regulation of epidermal growth factor-activated receptor activity NAS 11279102
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with SNX6: view

No data available for SIGNOR curated interactions for SNX6 Gene

Drugs & Compounds for SNX6 Gene

No Compound Related Data Available

Transcripts for SNX6 Gene

Unigene Clusters for SNX6 Gene

Sorting nexin 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNX6 Gene

No ASD Table

Relevant External Links for SNX6 Gene

GeneLoc Exon Structure for
SNX6
ECgene alternative splicing isoforms for
SNX6

Expression for SNX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SNX6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SNX6 Gene



Protein tissue co-expression partners for SNX6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SNX6 Gene:

SNX6

SOURCE GeneReport for Unigene cluster for SNX6 Gene:

Hs.356647

Evidence on tissue expression from TISSUES for SNX6 Gene

  • Nervous system(4.4)
  • Liver(4.3)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with SNX6: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNX6 Gene

Orthologs for SNX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SNX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNX6 34 35
  • 99.68 (n)
cow
(Bos Taurus)
Mammalia SNX6 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 35
  • 99 (a)
OneToMany
-- 35
  • 96 (a)
OneToMany
SNX6 34
  • 95.32 (n)
oppossum
(Monodelphis domestica)
Mammalia SNX6 35
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Snx6 35 16 34
  • 90.64 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Snx6 34
  • 90.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SNX6 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SNX6 34 35
  • 86.29 (n)
lizard
(Anolis carolinensis)
Reptilia SNX6 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia snx6 34
  • 78.63 (n)
zebrafish
(Danio rerio)
Actinopterygii snx6 34 35
  • 77.09 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004487 34
  • 58 (n)
fruit fly
(Drosophila melanogaster)
Insecta Snx6 34 35
  • 55.39 (n)
worm
(Caenorhabditis elegans)
Secernentea snx-6 34 35
  • 60.09 (n)
Y59A8B.22 36
  • 35 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5377 35
  • 46 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15264 34
Species where no ortholog for SNX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 SNX6 Gene

ENSEMBL:
Gene Tree for SNX6 (if available)
TreeFam:
Gene Tree for SNX6 (if available)

Paralogs for SNX6 Gene

Paralogs for SNX6 Gene

(2) SIMAP similar genes for SNX6 Gene using alignment to 8 proteins:

Pseudogenes.org Pseudogenes for SNX6 Gene

genes like me logo Genes that share paralogs with SNX6: view

Variants for SNX6 Gene

Sequence variations from dbSNP and Humsavar for SNX6 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000023701 -- 34,618,103(+) AATAA(C/T)TTTGA intron-variant
rs1000028236 -- 34,584,668(+) ACACT(C/G)TAACA intron-variant
rs1000053685 -- 34,577,007(+) ATTGA(A/G)CCACT intron-variant
rs1000068687 -- 34,596,212(+) ATTCT(A/G)TCTCC intron-variant
rs1000079788 -- 34,623,275(+) GGGGG(A/G)AAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SNX6 Gene

Variant ID Type Subtype PubMed ID
esv1007795 OTHER inversion 20482838
nsv1041857 CNV gain 25217958
nsv1049048 CNV gain 25217958
nsv1122887 CNV deletion 24896259
nsv479261 CNV novel sequence insertion 20440878
nsv499102 OTHER inversion 21111241
nsv523334 CNV loss 19592680
nsv7251 OTHER inversion 18451855
nsv93 OTHER inversion 15895083
nsv976326 CNV duplication 23825009
nsv977453 CNV duplication 23825009

Variation tolerance for SNX6 Gene

Residual Variation Intolerance Score: 21.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.48; 10.37% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SNX6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNX6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNX6 Gene

Disorders for SNX6 Gene

Relevant External Links for SNX6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNX6

No disorders were found for SNX6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNX6 Gene

Publications for SNX6 Gene

  1. Sorting nexin 6, a novel SNX, interacts with the transforming growth factor-beta family of receptor serine-threonine kinases. (PMID: 11279102) Parks W.T. … Lechleider R.J. (J. Biol. Chem. 2001) 2 3 4 22 64
  2. A large family of endosome-localized proteins related to sorting nexin 1. (PMID: 11485546) Teasdale R.D. … Gleeson P.A. (Biochem. J. 2001) 3 4 22 64
  3. Proteomic identification of sorting nexin 6 as a negative regulator of BACE1-mediated APP processing. (PMID: 20354142) Okada H. … Kim T.W. (FASEB J. 2010) 3 4 64
  4. Sorting nexin 6 interacts with breast cancer metastasis suppressor-1 and promotes transcriptional repression. (PMID: 20830743) Rivera J. … Bravo J. (J. Cell. Biochem. 2010) 3 4 64
  5. The retromer coat complex coordinates endosomal sorting and dynein-mediated transport, with carrier recognition by the trans-Golgi network. (PMID: 19619496) Wassmer T. … Cullen P.J. (Dev. Cell 2009) 3 4 64

Products for SNX6 Gene

Sources for SNX6 Gene

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