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

SOX9 Gene

protein-coding   GIFtS: 65
GCID: GC17P070117

SRY (sex determining region Y)-box 9

(Previous names: campomelic dysplasia, autosomal sex-reversal )
(Previous symbols: CMD1, CMPD1)
 Explore 59 diseases affiliated with
SOX9 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SOX9    

Aliases
for SOX9 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
SRY (Sex Determining Region Y)-Box 91 2     Campomelic Dysplasia, Autosomal Sex-Reversal1
CMD11 2 5     SRY (Sex-Determining Region Y)-Box 9 Protein2
SRA11 2 5     SRY-Related HMG-Box, Gene 92
CMPD11 2     Transcription Factor SOX-92

External Ids:    HGNC: 112041   Entrez Gene: 66622   Ensembl: ENSG000001253987   OMIM: 6081605   UniProtKB: P484363   

Export aliases for SOX9 gene to outside databases

Previous GC identifers: GC17P069873 GC17P073111 GC17P070581 GC17P070714 GC17P067628 GC17P065510


Summaries
for SOX9 gene

(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 SOX9:
The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class
DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates
transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome
campomelic dysplasia, frequently with sex reversal. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
Function: Plays an important role in the normal skeletal development. May regulate the expression of other genes
involved in chondrogenesis by acting as a transcription factor for these genes

Gene Wiki entry for SOX9


Genomic Views
for SOX9 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010783.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SOX9 gene promoter:
         PPAR-gamma1   SRY   MyoD   Sox9   Nkx2-5   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SOX9 promoter sequence
   Search SABiosciences Chromatin IP Primers for SOX9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SOX9


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

Entrez Gene cytogenetic band: 17q23   Ensembl cytogenetic band:  17q24.3   HGNC cytogenetic band: 17q23

SOX9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SOX9 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P070117:  view genomic region     (about GC identifiers)

Start:
 70,117,161 bp from pter      End:
 70,122,561 bp from pter
Size:
 5,401 bases      Orientation:
 plus strand

Proteins
for SOX9 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436 (See protein sequence)
Recommended Name: Transcription factor SOX-9  
Size: 509 amino acids; 56137 Da
Subcellular location: Nucleus (Potential)
3 PDB 3D structures from and Proteopedia for SOX9:
1S9M (3D)        1SX9 (3D)        4EUW (3D)    
Secondary accessions: Q53Y80

Explore the universe of human proteins at neXtProt for SOX9: NX_P48436

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P48436

    • SOX9 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_000337.1  
    ENSEMBL proteins: 
     ENSP00000245479  

    Human Recombinant Protein Products: 
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    Novus Biologicals SOX9 Proteins
    Novus Biologicals SOX9 Lysate
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    ProSpec Recombinant Protein for SOX9
    Uscn Proteins for SOX9

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0016585chromatin remodeling complex ----
    GO:0043234protein complex IDA--


    SOX9 for ontologies           About GeneDecksing



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    ThermoFisher Antibodies for SOX9

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    Uscn ELISAs and CLIAs for SOX9

    Protein Domains /
    Families
    for SOX9 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SOX9 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR009071 HMG_superfamily
     IPR022151 Sox_N

    Graphical View of Domain Structure for InterPro Entry P48436

    ProtoNet protein and cluster: P48436

    UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
    Similarity: Contains 1 HMG box DNA-binding domain


    Function
    for SOX9 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
    Function: Plays an important role in the normal skeletal development. May regulate the expression of other genes
    involved in chondrogenesis by acting as a transcription factor for these genes

         Genatlas biochemistry entry for SOX9:
    SRY related HMG box gene 9,expressed in the genital ridge of both sexes,in chondrocytes and in non-skeletal
    tissues,likely involved in the differentiation of Sertoli cells,potent activator of the chondrocyte-specific enhancer
    of COL2A1,required for cartilage formation,important mediator of the BMP2 and Indian hedgehog (IHH) sinaling pathways
    in osteogenic cells,modulator of LINE retroposons promoter activity

    miRNA
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    hsa-let-7b (MIRT005049)

    OriGene 3'-UTR Clone: SOX9
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SOX9
    8/68 QIAGEN miScript miRNA Assays for microRNAs that regulate SOX9 (see all 68):
    hsa-miR-582-3p hsa-miR-520f hsa-miR-300 hsa-miR-605 hsa-miR-485-3p hsa-miR-30d hsa-miR-3142 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmid: SOX9 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SOX9 (see all 4)
    OriGene shRNA RFP: SOX9
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SOX9

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: SOX9 (NM_000346)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX9 

    Cell Line
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    LifeMap BioReagents: cell lines associated with SOX9: PureStem 4D20.8, NCr-fac Progenitor,
    PureStem 7SMOO32, NCr-fac & Meso Progenitor, PureStem E15, Meso-prx/latp Progenitor, PureStem MEL2, NCr-fac Progenitor,
    PureStem SK11, NCr-fac & Meso-prx Progenitor, PureStem SM30, NCr-fac & Meso-latp Progenitor

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX9

    Gene Ontology (GO): 5/16 molecular function terms (GO ID links to tree view) (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000976transcription regulatory region sequence-specific DNA binding ----
    GO:0001046core promoter sequence-specific DNA binding IDA--
    GO:0001077RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA--
    GO:0001158enhancer sequence-specific DNA binding ISS--
    GO:0003677DNA binding ----


    SOX9 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for SOX9:
     Increased gamma-H2AX phosphory 

    Animal Models:
         Mouse knock-outs for SOX9: Sox9tm2.1Crm Sox9tm1.1Gsr
         15/24 MGI mutant phenotypes (inferred from 13 alleles) (MGI details for Sox9) (see all 24):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  growth/size  hearing/vestibular/ear  hematopoietic system 
     homeostasis/metabolism  immune system  integument  limbs/digits/tail  mortality/aging 

    SOX9 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for SOX9 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/6 super-pathways (see all 6) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Selected targets of ESR1
    		Selected targets of ESR11.00
    2Selected targets of CREB1
    		Selected targets of CREB11.00
    3Neural Crest Differentiation
    		Neural Crest Differentiation1.00
    4Endochondral Ossification
    		Endochondral Ossification1.00
    5Rho Family GTPases
    		Molecular Mechanisms of Cancer0.51

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    2 EMD Millipore Pathways for SOX9
        Selected targets of CREB1
    Selected targets of ESR1

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for SOX9
        Molecular Mechanisms of Cancer

    3 BioSystems Pathways for SOX9 
        Neural Crest Differentiation
    Endochondral Ossification
    Wnt Signaling Pathway NetPath



    SOX9 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SOX9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    5/25 Interacting proteins for SOX9 (P484363 ENSP000002454794) via UniProtKB, MINT, STRING, and/or I2D (see all 25)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HSPA1AP081073, ENSP000003648024I2D: score=3 STRING: ENSP00000364802
    SCXAQ7RTU73, ENSP000003455994I2D: score=1 STRING: ENSP00000345599
    NR5A1Q132853, ENSP000003626904I2D: score=4 STRING: ENSP00000362690
    HSPA1BP081073I2D: score=3 
    MAFO754443, ENSP000003270484I2D: score=3 STRING: ENSP00000327048
    About this table

    Gene Ontology (GO): 5/105 biological process terms (GO ID links to tree view) (see all 105):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development IMP8640233
    GO:0001502cartilage condensation ISS--
    GO:0001503ossification IEA--
    GO:0001658branching involved in ureteric bud morphogenesis IEA--
    GO:0001708cell fate specification ISS--


    SOX9 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SOX9 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SOX9 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SOX9
    10/21 Novoseek chemical compound relationships for SOX9 gene (see all 21)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    dmrt 70.8 2 16868052 (1), 19616114 (1)
    glycosaminoglycan 64.3 14 15639641 (2), 18163512 (1), 19096623 (1), 18985688 (1) (see all 11)
    alginate 53.1 3 19950204 (1), 15165474 (1), 17050539 (1)
    cmps 46.7 3 10213041 (1), 11076045 (1)
    testosterone 20.9 6 17234760 (2), 18190855 (2), 11097782 (1), 19535881 (1)
    ribonucleic acid 20.9 3 17518710 (1), 11710435 (1), 20157375 (1)
    chondroitin sulfate 18.3 8 18433381 (6)
    retinoic acid 16.5 17 19273910 (5), 19322650 (4), 10753864 (3), 15674337 (2) (see all 5)
    cytochalasin d 14.2 4 15665004 (1), 17050539 (1), 16565087 (1)
    dexamethasone 0.007 9 14753742 (3), 15734261 (3), 15009940 (1), 17690025 (1) (see all 5)

    Search CenterWatch for drugs/clinical trials and news about SOX9 

    Transcripts
    for SOX9 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SOX9 gene: 
    NM_000346.3  

    Unigene Cluster for SOX9:

    SRY (sex determining region Y)-box 9
    Hs.647409  [show with all ESTs]
    Unigene Representative Sequence: NM_000346
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000245479(uc002jiw.3)

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SOX9
    8/68 QIAGEN miScript miRNA Assays for microRNAs that regulate SOX9 (see all 68):
    hsa-miR-582-3p hsa-miR-520f hsa-miR-300 hsa-miR-605 hsa-miR-485-3p hsa-miR-30d hsa-miR-3142 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmid: SOX9 3' UTR sequence
    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AK295455.1 BC007951.2 BC018276.1 BC056420.1 BT006875.1 Z46629.1 

    4 DOTS entries:

    DT.416519  DT.95288976  DT.40299601  DT.97818151 

    24/205 AceView cDNA sequences (see all 205):

    BM762705 BU076661 AV681764 CK570306 AW183687 CK300183 CA773373 BC007951 
    N92393 AA628091 AA778589 BM698976 BM698241 BG697040 AA975310 AA400739 
    AA778708 W24710 BQ045441 BQ774016 BF343387 AA535677 AW080366 AA912521 

    GeneLoc Exon Structure


    Expression
    for SOX9 gene

    (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

    SOX9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGTCATCCAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SOX9 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/143 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 143) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    AdiposeCranial Subcutaneous White AdiposePreadipocytesAdipose
    AdiposeFacial Subcutaneous White AdiposePreadipocytesAdipose
    AdiposeSubcutaneous White AdiposePreadipocytesAdipose
    BoneAutopod Epiphyseal EndChondrocytesBone, Cartilage
    BoneAutopod Epiphyseal EndPrechondrocytesBone, Cartilage
    BoneAutopod Growth PlateHypertrophic ChondrocytesBone, Cartilage
    BoneCervical VertebraeChondrocytesBone, Cartilage
    BoneCervical VertebraeHypertrophic ChondrocytesBone, Cartilage
    BoneCervical VertebraeOsteochondro Mesenchymal CellsBone, Cartilage
    BoneCervical VertebraePrechondrocytesBone, Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10/37 LifeMap Cells (see all 37) 
    NameCategory
    PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor SM30 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor MEL2 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ mesenchymal progenitor E15 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    Sclerotome cells (Primary Cell)Bone, Cartilage, Somite
    PureStem™ progenitor SM22 (Embryonic Progenitor Cell)
    Osteoblast-like cells grown in a 3D culture system (Osteogenic different...)
    Chondrocyte-like cells (Direct differentiati...)Bone, Cartilage

    See SOX9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SOX9

    SOURCE GeneReport for Unigene cluster: Hs.647409
        SABiosciences Expression via Pathway-Focused PCR Arrays including SOX9: 
              Osteogenesis in human mouse rat
              Notch Signaling Targets in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              WNT Signaling Targets in human mouse rat
              Mesenchymal Stem Cell in human mouse rat

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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX9

    Orthologs
    for SOX9 gene

    (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.

    Orthologs for SOX9 gene from 6/18 species (see all 18)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SOX91 SRY (sex determining region Y)-box 9 86.4(n)
    90.06(a)    		   374148  NM_204281.1  NP_989612.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SOX96
    		 --
    		 80(a)
    		 1 ↔ 1
    		 GL343258.1(707274-714446)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.16902 Xenopus laevis transcription factor SOX9 mRNA, complete more 79.19(n)    AY035397.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii sox9a2 SRY-box containing gene 9a 80.59(n)   60641  AF277096.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta Sox100B1 , 3 DNA bending3
    CG15552-PA1    		 61(a)3
    50.64(n)1
    38.89(a)1    		   100B23
    450391  NM_143582.11  NP_651839.11 
    worm
    (Caenorhabditis elegans)    		 Secernentea sox-46
    		 Protein SOX-4
    		 22(a)
    		 possible ortholog
    		 X(3505427-3506378)


    ENSEMBL Gene Tree for SOX9 (if available)
    TreeFam Gene Tree for SOX9 (if available) 

    Paralogs
    for SOX9 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SOX9 gene
    SOX132  SOX22  SOX42  SOX12  SOX142  SOX32  SOX122  SOX152  
    SOX182  SOX52  ENSG000002587242  SOX212  SOX172  SOX62  SOX112  SOX82  
    SRY2  SOX102  SOX72  
    3 SIMAP similar genes for SOX9 using alignment to 1 protein entry:     SOX9_HUMAN:
    SOX10    SOX8    FLJ00094

    SOX9 for paralogs           About GeneDecksing



    Genomic Variants
    for SOX9 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/146 NCBI SNPs in SOX9 are shown (see all 146)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 17 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs22299891,2
    		C,F,H,non-pathogenic70118935(+) GACCAC/TCCGGA 2 H syn1 ese311Minor allele frequency- T:0.16MN NS EA NA EU 6339
    rs289402821,2
    		Cpathogenic70118921(+) TGCAGC/TACAAG 2 H Y mis1 ese32Minor allele frequency- T:0.00NA 4
    rs1048946471,2
    		Cpathogenic70118945(+) ATTACA/GAGTAC 2 K E mis10--------
    rs803386881,2
    		C,F,pathogenic70120318(+) CAGTAA/C/G/T 
                GACTA     		4 * Y stg1 syn11NA 4552
    rs1428026791,2
    		--70115257(+) TGCCCG/TATGGT 1 -- us2k10--------
    rs126017011,2
    		C,F,A,H,--70115358(+) ACTACG/ACGGAC 1 -- us2k122Minor allele frequency- A:0.33NS EA NA CSA WA 2245
    rs1165160231,2
    		F,--70115410(+) TGAAAG/ATAATC 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs795588521,2
    		F,--70115486(+) CCAGAA/GACATC 1 -- us2k11Minor allele frequency- G:0.09WA 118
    rs2012238681,2
    		--70115515(+) TCGTT-/AAAAAA 1 -- us2k10--------
    rs1445486021,2
    		--70115638(+) TTCTCC/TCGGAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SOX9 (70117161 - 70122561 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SOX9
         1 CNV: 5028
    Human Gene Mutation Database (HGMD): SOX9

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SOX9
    DNA2.0 Custom Variant and Variant Library Synthesis for SOX9

    Disorders / Diseases
    for SOX9 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    SOX9 for disorders           About GeneDecksing

    OMIM gene information: 608160   
    OMIM disorders: 114290  
    UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
  • Defects in SOX9 are the cause of campomelic dysplasia (CMD1) [MIM:114290]. CMD1 is a rare, often lethal,
    • dominantly inherited, congenital osteochondrodysplasia, associated with male-to-female autosomal sex reversal in
    two-thirds of the affected karyotypic males. A disease of the newborn characterized by congenital bowing and
    angulation of long bones, unusually small scapulae, deformed pelvis and spine and a missing pair of ribs. Craniofacial
    defects such as cleft palate, micrognatia, flat face and hypertelorism are common. Various defects of the ear are
    often evident, affecting the cochlea, malleus incus, stapes and tympanum. Most patients die soon after birth due to
    respiratory distress which has been attributed to hypoplasia of the tracheobronchial cartilage and small thoracic cage
  • Defects in SOX9 are the cause of 46,XX sex reversal type 2 (SRXX2) [MIM:278850]. SRXX2 is a condition in which
    • male gonads develop in a genetic female (female to male sex reversal)

    20/59 diseases for SOX9 (see all 59):    About MalaCards
    campomelic dysplasia    sex reversal    campomelic dysplasia with autosomal sex reversal    pierre robin sequence
    xy sex reversal    degenerative disc disease    swyer syndrome    gonadal dysgenesis
    disorders of sex development    mesenchymal chondrosarcoma    osteochondrodysplasia    achondroplasia
    virilization    mobius syndrome    frasier syndrome    sertoli cell tumor
    wilms tumor    dwarfism    synovial sarcoma    chondrosarcoma

    5 diseases from the University of Copenhagen DISEASES database for SOX9:
    Campomelic dysplasia     Osteoarthritis     Gonadal dysgenesis     Chondrosarcoma
    Hermaphroditism

    10/28 Novoseek disease relationships for SOX9 gene (see all 28)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    campomelic dysplasia 97.1 84 10072439 (3), 8894698 (2), 10364523 (2), 16467253 (2) (see all 55)
    osteochondrodysplasias 56.9 1 11008738 (1)
    swyer syndrome 56.1 2 9002675 (1)
    skeletal dysplasia 54.3 3 20392266 (1), 9119111 (1)
    osteoarthritis 52.5 5 17935617 (2), 17968906 (1), 20196777 (1), 18550917 (1)
    virilization 48.1 1 9452059 (1)
    pierre robin sequence 45.3 3 17551083 (2), 19473998 (1)
    chondrosarcoma 44.6 7 20039424 (2), 12681949 (2), 12673561 (1), 18438857 (1) (see all 5)
    dwarfism 44.2 2 8782821 (1), 11430871 (1)
    achondroplasia 43.5 1 10980415 (1)

    GeneTests: SOX9
    Campomelic Dysplasia

    Genetic Association Database (GAD): SOX9
    Human Genome Epidemiology (HuGE) Navigator: SOX9 (5 documents)

    Export disorders for SOX9 gene to outside databases

    Publications
    for SOX9 gene

    (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 SOX9 gene, integrated from 9 sources (see all 487):
    (articles sorted by number of sources associating them with SOX9)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Compound effects of point mutations causing campomelic dysplasia/autosomal sex reversal upon SOX9 structure, nuclear transport, DNA binding, and transcriptional activation. (PubMed id 11323423)1, 2, 9 Preiss S....Harley V.R. (2001)
    2. Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. (PubMed id 7485151)1, 2, 9 Kwok C.... Schafer A.J. (1995)
    3. Mutation analysis of five candidate genes in Chinese patients with hypospadias. (PubMed id 15266301)1, 4, 9 Wang Y....Shen Y. (2004)
    4. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. (PubMed id 8001137)1, 2, 9 Wagner T.... Scherer G. (1994)
    5. Heterozygous SOX9 mutations allowing for residual DNA -binding and transcriptional activation lead to the acampomelic variant of camp omelic dysplasia. (PubMed id 20513132)1, 2, 9 Staffler A....Holzinger A. (2010)
    6. Mutation analysis of SOX9 and single copy number vari ant analysis of the upstream region in eight patients with campomelic dysplasia and acampomelic campomelic dysplasia. (PubMed id 19921652)1, 2, 9 Wada Y....Ogata T. (2009)
    7. Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia. (PubMed id 12783851)1, 2, 9 Sock E....Scherer G. (2003)
    8. Acampomelic campomelic dysplasia with SOX9 mutation. (PubMed id 10951468)1, 2, 9 Thong M.K....Morris L. (2000)
    9. Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia. (PubMed id 10446171)1, 2, 9 McDowall S.... Harley V. (1999)
    10. Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations. (PubMed id 9002675)1, 2, 9 Meyer J.... Scherer G. (1997)

    External Searches for SOX9 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SOX9 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6662 HGNC: 11204 AceView: SOX9 Ensembl:ENSG00000125398 euGenes: HUgn6662
    ECgene: SOX9 H-InvDB: SOX9

    Other Databases showing SOX9 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SOX9 gene

    (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 SOX9 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SOX9

    Intellectual Property
    for SOX9 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SOX9 gene:
    Search GeneIP for patents involving SOX9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for SOX9 gene

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     SOX9 Proteins, Antibodies, CLIAs, and ELISAs
     Cell Lines associated with SOX9: PureStem 4D20.8, NCr-fac Progenitor,
    PureStem 7SMOO32, NCr-fac & Meso Progenitor, PureStem E15, Meso-prx/latp Progenitor, PureStem MEL2, NCr-fac Progenitor,
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