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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SNX12 Gene

protein-coding   GIFtS: 51
GCID: GC0XM070276

Sorting Nexin 12

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Sorting Nexin 121 2
Sorting Nexin-122

External Ids:    HGNC: 149761   Entrez Gene: 299342   Ensembl: ENSG000001471647   OMIM: 3008835   UniProtKB: Q9UMY43   

Export aliases for SNX12 gene to outside databases

Previous GC identifers: GC0XM066458 GC0XM067758 GC0XM068511 GC0XM069147 GC0XM070063 GC0XM070192 GC0XM070197 GC0XM064099


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SNX12 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 some family members. A similar protein in mouse may be involved in regulating
the neurite outgrowth. Alternate splicing results in multiple transcript variants. (provided by RefSeq, Jan 2012)

GeneCards Summary for SNX12 Gene: 
SNX12 (sorting nexin 12) is a protein-coding gene. Diseases associated with SNX12 include cerebritis, and neuronitis. GO annotations related to this gene include protein binding and phosphatidylinositol binding. An important paralog of this gene is SNX10.

UniProtKB/Swiss-Prot: SNX12_HUMAN, Q9UMY4
Function: May be involved in several stages of intracellular trafficking (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NT_011669.17  NC_018934.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNX12 gene promoter:
         TBP   C/EBPbeta   FOXF2   p53   COMP1   TFIID   HFH-1   c-Myb   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSNX12 promoter sequence
   Search SABiosciences Chromatin IP Primers for SNX12

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNX12


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq13.1   Ensembl cytogenetic band:  Xq13.1   HGNC cytogenetic band: Xq13.1

SNX12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNX12 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM070276:  view genomic region     (about GC identifiers)

Start:
70,279,094 bp from pter      End:
70,288,273 bp from pter
Size:
9,180 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SNX12_HUMAN, Q9UMY4 (See protein sequence)
Recommended Name: Sorting nexin-12  
Size: 172 amino acids; 19730 Da
Subcellular location: Membrane; Peripheral membrane protein; Cytoplasmic side (Potential)
1 PDB 3D structure from and Proteopedia for SNX12:
2CSK (3D)    
Secondary accessions: F8W8K5 Q8WUG9
Alternative splicing: 3 isoforms:  Q9UMY4-1   Q9UMY4-2   Q9UMY4-3   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for SNX12: NX_Q9UMY4

Explore proteomics data for SNX12 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9UMY4

  • SNX12 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SNX12 Protein Expression
    REFSEQ proteins (5 alternative transcripts): 
    NP_001243114.1  NP_001243115.1  NP_001243116.1  NP_001243117.1  NP_037478.2  

    ENSEMBL proteins: 
     ENSP00000363392   ENSP00000276105  

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    Browse Sino Biological Recombinant Proteins
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SNX12 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane IEA--

    SNX12 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    SNX: Sorting nexins

    1 InterPro protein domain:
     IPR001683 Phox

    Graphical View of Domain Structure for InterPro Entry Q9UMY4

    ProtoNet protein and cluster: Q9UMY4

    1 Blocks protein domain: IPB001683 Phox-like

    UniProtKB/Swiss-Prot: SNX12_HUMAN, Q9UMY4
    Domain: The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3-phosphate (By
    similarity)
    Similarity: Belongs to the sorting nexin family
    Similarity: Contains 1 PX (phox homology) domain


    SNX12 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SNX12_HUMAN, Q9UMY4
    Function: May be involved in several stages of intracellular trafficking (By similarity)

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17474147
    GO:0035091phosphatidylinositol binding IEA--
         
    SNX12 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SNX12:
     Synthetic lethal with c-Myc af 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Snx12):
     normal 

    SNX12 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SNX12 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SNX12

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    5/564 Interacting proteins for SNX12 (Q9UMY41, 2, 3 ENSP000003633924) via UniProtKB, MINT, STRING, and/or I2D (see all 564)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NCK1P163331, 3, ENSP000002889864EBI-1752602,EBI-389883 I2D: score=1 STRING: ENSP00000288986
    ABL1P005193, ENSP000003614234I2D: score=1 STRING: ENSP00000361423
    GRB2P629933, ENSP000003390074I2D: score=1 STRING: ENSP00000339007
    CDC5LQ994592, ENSP000003605324MINT-7947479 STRING: ENSP00000360532
    FYNP062413, ENSP000003576564I2D: score=1 STRING: ENSP00000357656
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007154cell communication IEA--
    GO:0015031protein transport IEA--

    SNX12 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SNX12

    Search CenterWatch for drugs/clinical trials and news about SNX12

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SNX12 gene (5 alternative transcripts): 
    NM_001256185.1  NM_001256186.1  NM_001256187.1  NM_001256188.1  NM_013346.3  

    Unigene Cluster for SNX12:

    Sorting nexin 12
    Hs.260750  [show with all ESTs]
    Unigene Representative Sequence: NM_001256185
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000483560 ENST00000374274(uc004dyp.1 uc004dyr.1) ENST00000490561
    ENST00000465030 ENST00000276105
    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate SNX12:
    hsa-miR-4280
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    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SNX12

    Additional mRNA sequence: 

    AF171229.1 AK025781.1 AK312977.1 BC024301.1 BC033809.1 BC044059.1 BC063716.1 BC080535.1 
    BC103847.2 BC103848.1 BC108323.1 BT007203.1 

    10 DOTS entries:

    DT.453894  DT.121323354  DT.100811966  DT.100811972  DT.100842384  DT.100811961  DT.91774879  DT.97818329 
    DT.91765745  DT.100811969 

    24/282 AceView cDNA sequences (see all 282):

    AI457133 BM786515 T30489 CF131335 BM794354 BM841021 BC024301 BU183048 
    BX346272 AL558606 BC063716 BU682830 BQ879283 AI341920 AI891005 AI719178 
    AI192201 AI332882 CR594125 AA027151 AA447839 BI518693 AI829483 BM835593 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for SNX12 (see all 6)    About this scheme

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


    ECgene alternative splicing isoforms for SNX12

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SNX12 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAAGATTGG
    SNX12 Expression
    About this image


    See SNX12 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SNX12

    SOURCE GeneReport for Unigene cluster: Hs.260750
        SABiosciences Custom PCR Arrays for SNX12
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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

    Orthologs for SNX12 gene from 8/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Snx121 , 5 sorting nexin 121, 5 94.24(n)1
    100(a)1
      X (43.72 cM)5
    559881  NM_001110310.11  NP_001103780.11 
     1010977865 
    chicken
    (Gallus gallus)
    Aves SNX121 sorting nexin 12 84.16(n)
    94.44(a)
      428704  NM_001031533.1  NP_001026704.1 
    lizard
    (Anolis carolinensis)
    Reptilia SNX126
    Uncharacterized protein
    96(a)
    1 ↔ 1
    GL343758.1(146813-157717)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ039788.12   -- 80.98(n)    BJ039788.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC044462.12   -- 76.91(n)   394098  BC044462.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG63591 , 3 intracellular protein transport3
    CG63591
    77(a)3
    71.25(n)1
    78.12(a)1
      87C33
    415511  NM_141957.31  NP_650214.11 
    worm
    (Caenorhabditis elegans)
    Secernentea W06D4.53
    snx-31
    PhoX homologous domain, present in
    p47phox and more3
    Protein SNX-31
    71(a)3
    65.58(n)1
    71.9(a)1
      I(9071506-9072611)3
    1892401  NM_060036.11  NP_492437.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SNX36
    Sorting nexin required to maintain late-Golgi resi...
    36(a)
    1 → many
    XV(1009224-1009712)


    ENSEMBL Gene Tree for SNX12 (if available)
    TreeFam Gene Tree for SNX12 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SNX12 gene
    SNX102  SNX32  SNX112  
    5 SIMAP similar genes for SNX12 using alignment to 2 protein entries:     SNX12_HUMAN (see all proteins):
    SNX3    SNX11    SNX10    SNX1    SNX30

    SNX12 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/240 SNPs in SNX12 are shown (see all 240)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs736348571,2
    C,F--70278826(+) AACCAG/AATCTG 5 -- ds50011Minor allele frequency- A:0.00WA 2
    rs1408567401,2
    --70279070(+) TAAATC/TTACAA 5 -- ds50010--------
    rs111341,2
    F--70279169(+) TGCTGA/GATAAA 5 -- ut31 ese31Minor allele frequency- G:0.00MN 184
    rs115491301,2
    C,F--70279172(+) TGAATA/TAAAGC 5 -- ut312Minor allele frequency- T:0.33NA CSA 3
    rs115491291,2
    C,F--70279177(+) AAAAGC/GCCCGA 5 -- ut315Minor allele frequency- G:0.09NA MN 322
    rs1413643521,2
    --70279212(+) AATGGC/GGCCTC 5 -- ut310--------
    rs1842990941,2
    --70279254(+) GAAATC/TGTTTT 5 -- ut310--------
    rs1899090911,2
    --70279272(+) TGTCTA/GTAACA 5 -- ut310--------
    rs1932033611,2
    --70279366(+) CCCTGG/TCGCAG 5 -- ut310--------
    rs67801,2
    C,F,O,A,H--70279492(+) TTTCCA/CCAGTG 5 -- ut31 ese321Minor allele frequency- C:0.60MN NS EA WA NA 2776

    HapMap Linkage Disequilibrium report for SNX12 (70279094 - 70288273 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SNX12:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv6952CNV Insertion18451855
    esv33082CNV Loss17666407
    esv1584074OTHER Inversion17803354

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 300883    OMIM disorders: --

    2 diseases for SNX12:    About MalaCards
    cerebritis    neuronitis


    SNX12 for disorders           About GeneDecksing


    Export disorders for SNX12 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SNX12 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with SNX12)
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    1. A large family of endosome-localized proteins related to sorting nexin 1. (PubMed id 11485546)1, 2, 9 Teasdale R.D.... Gleeson P.A. (2001)
    2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    3. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (2005)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    7. SNX12 role in endosome membrane transport. (PubMed id 22719997)1 Pons V....Gruenberg J. (2012)
    8. Sorting nexin 12 interacts with BACE1 and regulates BA CE1-mediated APP processing. (PubMed id 22709416)1 Zhao Y....Zhang Y.W. (2012)
    9. Expression of sorting nexin 12 is regulated in develo ping cerebral cortical neurons. (PubMed id 22109349)1 Mizutani R....Tanoue A. (2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 29934 HGNC: 14976 AceView: SNX12 Ensembl:ENSG00000147164 euGenes: HUgn29934
    ECgene: SNX12 H-InvDB: SNX12

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SNX12 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SNX12 gene:
    Search GeneIP for patents involving SNX12

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