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Aliases for SOX9 Gene

Aliases for SOX9 Gene

  • SRY-Box 9 2 3 5
  • SRY (Sex-Determining Region Y)-Box 9 Protein 3
  • Campomelic Dysplasia, Autosomal Sex-Reversal 2
  • SRY (Sex Determining Region Y)-Box 9 2
  • SRY (Sex Determining Region Y)-Box9 3
  • SRY-Related HMG-Box, Gene 9 3
  • Transcription Factor SOX-9 3
  • SRY Box 9 2
  • SRXY10 3
  • SRXX2 3
  • CMPD1 3
  • SRA1 3
  • CMD1 3

External Ids for SOX9 Gene

Previous HGNC Symbols for SOX9 Gene

  • CMD1
  • CMPD1

Previous GeneCards Identifiers for SOX9 Gene

  • GC17P069873
  • GC17P073111
  • GC17P070581
  • GC17P070714
  • GC17P067628
  • GC17P070117
  • GC17P065510

Summaries for SOX9 Gene

Entrez Gene Summary for SOX9 Gene

  • 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]

GeneCards Summary for SOX9 Gene

SOX9 (SRY-Box 9) is a Protein Coding gene. Diseases associated with SOX9 include Campomelic Dysplasia and 46,Xy Sex Reversal 10. Among its related pathways are Signaling by Wnt and ERK Signaling. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and protein kinase activity. An important paralog of this gene is SOX10.

UniProtKB/Swiss-Prot for SOX9 Gene

  • Transcriptional regulator (PubMed:24038782). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with ZNF219 (By similarity). Plays a role in chondrocyte differentiation (By similarity). Important for normal skeletal development (PubMed:24038782).

Gene Wiki entry for SOX9 Gene

Additional gene information for SOX9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX9 Gene

Genomics for SOX9 Gene

GeneHancer (GH) Regulatory Elements for SOX9 Gene

Promoters and enhancers for SOX9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J072120 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.7 +2.8 2808 8.6 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 SOX9 SLC39A11 GC17P072122 GC17P072161 SOX9-AS1
GH17J072119 Enhancer 0.5 ENCODE 650.7 -1.8 -1805 0.2 CTCF SSRP1 ZGPAT BMI1 SOX9 LINC02097 SOX9-AS1
GH17J072418 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 6.7 +300.9 300854 5.9 HDGF PKNOX1 FOXA2 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 C17orf80 SOX9 ENSG00000263680 LINC02003 LINC00673 LINC00511
GH17J072715 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 6 +595.2 595165 1.8 ELF3 FOXA2 KLF17 SIN3A RARA FOS SMARCC1 CEBPB ELF1 REST GC17P072715 SOX9 SLC39A11 GC17P072756
GH17J072385 Enhancer 1.1 ENCODE dbSUPER 5 +266.2 266157 2.5 FOXA2 MLX ARID4B FEZF1 ZNF121 KLF7 FOS NFKBIZ SP5 ZHX2 LINC00511 SOX9 ENSG00000263680 LINC02003
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX9 gene promoter:
  • SRY
  • Sox9
  • PPAR-gamma1
  • PPAR-gamma2
  • Nkx2-5
  • MyoD

Genomic Locations for SOX9 Gene

Genomic Locations for SOX9 Gene
5,401 bases
Plus strand
5,401 bases
Plus strand

Genomic View for SOX9 Gene

Genes around SOX9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX9 Gene

Proteins for SOX9 Gene

  • Protein details for SOX9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transcription factor SOX-9
    Protein Accession:
    Secondary Accessions:
    • Q53Y80

    Protein attributes for SOX9 Gene

    509 amino acids
    Molecular mass:
    56137 Da
    Quaternary structure:
    • Interacts (via C-terminus) with ZNF219.

    Three dimensional structures from OCA and Proteopedia for SOX9 Gene

neXtProt entry for SOX9 Gene

Post-translational modifications for SOX9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SOX9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for SOX9

No data available for DME Specific Peptides for SOX9 Gene

Domains & Families for SOX9 Gene

Gene Families for SOX9 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX9 Gene

Suggested Antigen Peptide Sequences for SOX9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SOX9: view

No data available for UniProtKB/Swiss-Prot for SOX9 Gene

Function for SOX9 Gene

Molecular function for SOX9 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator (PubMed:24038782). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with ZNF219 (By similarity). Plays a role in chondrocyte differentiation (By similarity). Important for normal skeletal development (PubMed:24038782).
GENATLAS Biochemistry:
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

Phenotypes From GWAS Catalog for SOX9 Gene

Gene Ontology (GO) - Molecular Function for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS,IEA 19274049
GO:0001046 core promoter sequence-specific DNA binding IDA 20530484
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA,IEA 20484372
GO:0001158 enhancer sequence-specific DNA binding IEA,ISS --
genes like me logo Genes that share ontologies with SOX9: view
genes like me logo Genes that share phenotypes with SOX9: view

Human Phenotype Ontology for SOX9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SOX9 Gene

MGI Knock Outs for SOX9:
  • Sox9 Sox9<tm2.1Crm>
  • Sox9 Sox9<tm1Crm>
  • Sox9 Sox9<tm1.1Gsr>
  • Sox9 Sox9<tm2.1Haak>
  • Sox9 Sox9<tm2.1Tlu>

Transcription Factor Targets for SOX9 Gene

Selected GeneGlobe predicted Target genes for SOX9
Targeted motifs for SOX9 Gene
HOMER Transcription Factor Regulatory Elements motif SOX9
  • Consensus sequence: AGGVNCCTTTGT Submotif: canonical Cell Type: Limb GEO ID: GSE73225

Clone Products

  • Addgene plasmids for SOX9

No data available for Enzyme Numbers (IUBMB) for SOX9 Gene

Localization for SOX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX9 Gene

Subcellular locations from

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 SOX9 gene
Compartment Confidence
nucleus 5
extracellular 3
cytoskeleton 2
plasma membrane 1
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 8640233
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IEA --
GO:0032991 protein-containing complex IDA 20530484
GO:0044798 nuclear transcription factor complex IEA --
genes like me logo Genes that share ontologies with SOX9: view

Pathways & Interactions for SOX9 Gene

genes like me logo Genes that share pathways with SOX9: view

SIGNOR curated interactions for SOX9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 8640233
GO:0001502 cartilage condensation ISS,IEA --
GO:0001503 ossification IEA --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001708 cell fate specification IEA,ISS --
genes like me logo Genes that share ontologies with SOX9: view

Drugs & Compounds for SOX9 Gene

(11) Drugs for SOX9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(10) Additional Compounds for SOX9 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SOX9: view

Transcripts for SOX9 Gene

mRNA/cDNA for SOX9 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(205) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SOX9 Gene

SRY (sex determining region Y)-box 9:
Representative Sequences:

Clone Products

  • Addgene plasmids for SOX9

Alternative Splicing Database (ASD) splice patterns (SP) for SOX9 Gene

No ASD Table

Relevant External Links for SOX9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SOX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SOX9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX9 Gene

This gene is overexpressed in Minor Salivary Gland (x4.1).

Protein differential expression in normal tissues from HIPED for SOX9 Gene

This gene is overexpressed in Monocytes (42.6), Fetal testis (16.8), and Testis (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SOX9 Gene

Protein tissue co-expression partners for SOX9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SOX9 Gene:


SOURCE GeneReport for Unigene cluster for SOX9 Gene:


Evidence on tissue expression from TISSUES for SOX9 Gene

  • Nervous system(4.7)
  • Eye(4.4)
  • Bone(2.7)
  • Intestine(2.6)
  • Pancreas(2.4)
  • Heart(2.3)
  • Kidney(2.3)
  • Muscle(2.3)
  • Bone marrow(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX9 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • larynx
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • pituitary gland
  • scalp
  • skull
  • tongue
  • vocal cord
  • breast
  • bronchus
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
  • kidney
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • placenta
  • prostate
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vas deferens
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SOX9: view

No data available for mRNA Expression by UniProt/SwissProt for SOX9 Gene

Orthologs for SOX9 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SOX9 34 33
  • 99.87 (n)
(Canis familiaris)
Mammalia SOX9 34 33
  • 93.52 (n)
(Bos Taurus)
Mammalia SOX9 34 33
  • 91.09 (n)
(Monodelphis domestica)
Mammalia SOX9 34
  • 90 (a)
(Mus musculus)
Mammalia Sox9 16 34 33
  • 89.35 (n)
(Rattus norvegicus)
Mammalia Sox9 33
  • 89.02 (n)
(Ornithorhynchus anatinus)
Mammalia SOX9 34
  • 88 (a)
(Gallus gallus)
Aves SOX9 34 33
  • 85.58 (n)
(Anolis carolinensis)
Reptilia SOX9 34
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sox9 33
  • 77.59 (n)
Str.15584 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.1690 33
(Danio rerio)
Actinopterygii sox9a 34 33 33
  • 76.81 (n)
sox9b 34
  • 68 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11885 33
fruit fly
(Drosophila melanogaster)
Insecta Sox100B 34 35
  • 28 (a)
(Caenorhabditis elegans)
Secernentea sox-4 34
  • 34 (a)
Species where no ortholog for SOX9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SOX9 Gene

Gene Tree for SOX9 (if available)
Gene Tree for SOX9 (if available)
Evolutionary constrained regions (ECRs) for SOX9: view image

Paralogs for SOX9 Gene

(3) SIMAP similar genes for SOX9 Gene using alignment to 12 proteins:

  • U5XK44_HUMAN
  • U5XK50_HUMAN
  • U5XN63_HUMAN
  • U5XN67_HUMAN
genes like me logo Genes that share paralogs with SOX9: view

Variants for SOX9 Gene

Sequence variations from dbSNP and Humsavar for SOX9 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1042667 benign, Camptomelic dysplasia 72,124,410(+) A/C 3_prime_UTR_variant
rs1042673 benign, Camptomelic dysplasia 72,125,198(+) A/G 3_prime_UTR_variant
rs1042678 benign, Camptomelic dysplasia 72,125,967(+) G/A 3_prime_UTR_variant
rs1042837249 uncertain-significance, Camptomelic dysplasia 72,121,189(+) C/G 5_prime_UTR_variant
rs104894647 pathogenic, Acampomelic campomelic dysplasia, Campomelic dysplasia (CMD1) [MIM:114290] 72,122,804(+) A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for SOX9 Gene

Variant ID Type Subtype PubMed ID
esv3573809 CNV gain 25503493
nsv833530 CNV gain+loss 17160897

Variation tolerance for SOX9 Gene

Residual Variation Intolerance Score: 9.81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.75; 15.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOX9 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX9 Gene

Disorders for SOX9 Gene

MalaCards: The human disease database

(33) MalaCards diseases for SOX9 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SOX9 in MalaCards View complete list of genes associated with diseases


  • Campomelic dysplasia (CMD1) [MIM:114290]: A rare, often lethal, osteochondrodysplasia characterized by congenital bowing and angulation of long bones. Other skeletal defects include unusually small scapula, deformed pelvis and spine, and a missing pair of ribs. Craniofacial and ear defects are common. Most patients die soon after birth due to respiratory distress which has been attributed to hypoplasia of the tracheobronchial cartilage and small thoracic cage. Up to two-thirds of affected XY individuals have genital defects or may develop as phenotypic females. {ECO:0000269 PubMed:10446171, ECO:0000269 PubMed:10951468, ECO:0000269 PubMed:11323423, ECO:0000269 PubMed:11754051, ECO:0000269 PubMed:12783851, ECO:0000269 PubMed:19033726, ECO:0000269 PubMed:19921652, ECO:0000269 PubMed:20513132, ECO:0000269 PubMed:24038782, ECO:0000269 PubMed:7485151, ECO:0000269 PubMed:9002675, ECO:0000269 PubMed:9452059}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 46,XX sex reversal 2 (SRXX2) [MIM:278850]: A condition in which male gonads develop in a genetic female (female to male sex reversal). {ECO:0000269 PubMed:21208124}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 46,XY sex reversal 10 (SRXY10) [MIM:616425]: A disorder of sex development. Affected individuals have a 46,XY karyotype, show gonadal dysgenesis with streak gonads, look like normal females at birth, do not develop secondary sexual characteristics at puberty and do not menstruate. {ECO:0000269 PubMed:25604083}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SOX9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SOX9: view

No data available for Genatlas for SOX9 Gene

Publications for SOX9 Gene

  1. Compound effects of point mutations causing campomelic dysplasia/autosomal sex reversal upon SOX9 structure, nuclear transport, DNA binding, and transcriptional activation. (PMID: 11323423) Preiss S … Harley VR (The Journal of biological chemistry 2001) 3 4 22 58
  2. Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia. (PMID: 10446171) McDowall S … Harley V (The Journal of biological chemistry 1999) 3 4 22 58
  3. Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. (PMID: 7485151) Kwok C … Young ID (American journal of human genetics 1995) 3 4 22 58
  4. Copy number variation of two separate regulatory regions upstream of SOX9 causes isolated 46,XY or 46,XX disorder of sex development. (PMID: 25604083) Kim GJ … Scherer G (Journal of medical genetics 2015) 3 4 58
  5. A novel SOX9 H169Q mutation in a family with overlapping phenotype of mild campomelic dysplasia and small patella syndrome. (PMID: 24038782) Matsushita M … Nishimura G (American journal of medical genetics. Part A 2013) 3 4 58

Products for SOX9 Gene