P48436 (SOX9_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcription factor SOX-9

Gene names

Name:

SOX9

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	509 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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.
Subcellular location	Nucleus Potential.
Involvement in disease	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. Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 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). Ref.6
Sequence similarities	Contains 1 HMG box DNA-binding domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Disease	Disease mutation
Ligand	DNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ERK1 and ERK2 cascade Inferred from sequence or structural similarity. Source: UniProtKB cAMP-mediated signaling Inferred from direct assay. Source: UniProtKB cartilage condensation Inferred from sequence or structural similarity. Source: UniProtKB cell fate specification Inferred from sequence or structural similarity. Source: UniProtKB cellular response to epidermal growth factor stimulus Inferred from sequence or structural similarity. Source: UniProtKB cellular response to heparin Inferred from sequence or structural similarity. Source: UniProtKB cellular response to interleukin-1 Inferred from expression pattern. Source: UniProtKB cellular response to mechanical stimulus Inferred from sequence or structural similarity. Source: UniProtKB cellular response to retinoic acid Inferred from expression pattern. Source: UniProtKB cellular response to transforming growth factor beta stimulus Inferred from direct assay. Source: UniProtKB chondrocyte differentiation involved in endochondral bone morphogenesis Inferred from mutant phenotype. Source: UniProtKB chondrocyte hypertrophy Inferred from sequence or structural similarity. Source: UniProtKB chromatin remodeling Inferred from direct assay. Source: UniProtKB cochlea morphogenesis Inferred from sequence or structural similarity. Source: UniProtKB endocardial cushion morphogenesis Inferred from sequence or structural similarity. Source: UniProtKB epidermal growth factor receptor signaling pathway Inferred from sequence or structural similarity. Source: UniProtKB epithelial cell proliferation involved in prostatic bud elongation Inferred from sequence or structural similarity. Source: UniProtKB epithelial to mesenchymal transition Inferred from sequence or structural similarity. Source: UniProtKB hair follicle development Inferred from sequence or structural similarity. Source: UniProtKB intestinal epithelial structure maintenance Inferred from sequence or structural similarity. Source: UniProtKB male germ-line sex determination Inferred from sequence or structural similarity. Source: UniProtKB metanephric nephron tubule formation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of apoptotic process Inferred from mutant phenotype. Source: UniProtKB negative regulation of canonical Wnt receptor signaling pathway Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of chondrocyte differentiation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of epithelial cell proliferation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of immune system process Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of myoblast differentiation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of photoreceptor cell differentiation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from mutant phenotype. Source: UniProtKB nucleosome assembly Inferred from direct assay. Source: UniProtKB otic vesicle formation Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of branching involved in ureteric bud morphogenesis Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of cartilage development Inferred from direct assay. Source: UniProtKB positive regulation of chondrocyte differentiation Inferred from direct assay. Source: UniProtKB positive regulation of epithelial cell differentiation Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of epithelial cell migration Inferred from mutant phenotype. Source: UniProtKB positive regulation of epithelial cell proliferation Inferred from expression pattern. Source: UniProtKB positive regulation of male gonad development Inferred from direct assay. Source: UniProtKB positive regulation of mesenchymal cell proliferation Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of mesenchymal stem cell differentiation Inferred from direct assay. Source: UniProtKB positive regulation of phosphatidylinositol 3-kinase cascade Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of protein phosphorylation Inferred from sequence or structural similarity. Source: UniProtKB protein complex assembly Inferred from direct assay. Source: UniProtKB regulation of cell cycle process Inferred from mutant phenotype. Source: UniProtKB regulation of cell proliferation involved in tissue homeostasis Inferred from sequence or structural similarity. Source: UniProtKB renal vesicle induction Inferred from sequence or structural similarity. Source: UniProtKB retinal rod cell differentiation Inferred from sequence or structural similarity. Source: UniProtKB somatic stem cell maintenance Inferred from sequence or structural similarity. Source: UniProtKB spermatogenesis Inferred from sequence or structural similarity. Source: UniProtKB
Cellular component	chromatin remodeling complex Inferred from direct assay. Source: UniProtKB
Molecular function	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription Inferred from direct assay. Source: UniProtKB chromatin binding Inferred from direct assay. Source: UniProtKB core promoter sequence-specific DNA binding Inferred from direct assay. Source: UniProtKB enhancer sequence-specific DNA binding Inferred from sequence or structural similarity. Source: UniProtKB protein kinase A catalytic subunit binding Inferred from physical interaction. Source: UniProtKB protein kinase activity Inferred from sequence or structural similarity. Source: UniProtKB sequence-specific distal enhancer binding RNA polymerase II transcription factor activity Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 509	509	Transcription factor SOX-9		PRO_0000048739
Regions
	DNA binding	105 – 173	69	HMG box
	Compositional bias	339 – 378	40	Gln/Pro-rich
	Compositional bias	342 – 346	5	Poly-Pro
Natural variations
	Natural variant	76	1	A → E in CMD1; dimerization and the resulting capacity to activate promoters via dimeric binding sites is lost; other features of the protein function remain unaltered. Ref.15		VAR_063642
	Natural variant	108	1	P → L in CMD1. Ref.9		VAR_003735
	Natural variant	112	1	F → L in CMD1; loss of DNA binding. Ref.8 Ref.11		VAR_003736
	Natural variant	112	1	F → S in CMD1. Ref.10		VAR_003737
	Natural variant	113	1	M → T in CMD1. Ref.16		VAR_063643
	Natural variant	113	1	M → V in CMD1; residual DNA binding and transactivation of regulated genes. Ref.17		VAR_063644
	Natural variant	119	1	A → V in CMD1; almost no loss of DNA binding. Ref.8 Ref.11		VAR_003738
	Natural variant	143	1	W → R in CMD1. Ref.9		VAR_003739
	Natural variant	152	1	R → P in CMD1. Ref.9		VAR_003740
	Natural variant	154	1	F → L in CMD1; 5% of wild-type DNA binding actvity; transcriptional activation is only reduced to 26% of wild-type activity. Ref.14		VAR_008529
	Natural variant	158	1	A → T in CMD1; 17% of wild-type DNA binding activity; shows a 2-fold reduction in nuclear import efficiency; transcriptional activation is only reduced to 62% of wild-type activity. Ref.14		VAR_008530
	Natural variant	165	1	H → Q in CMD1; residual DNA binding and transactivation of regulated genes. Ref.17		VAR_063645
	Natural variant	165	1	H → Y in CMD1; loss of DNA binding. Ref.11 Ref.13 Corresponds to variant rs28940282 [ dbSNP | Ensembl ].		VAR_008531
	Natural variant	170	1	P → L in CMD1. Ref.16		VAR_063646
	Natural variant	170	1	P → R in CMD1. Ref.9 Ref.11		VAR_003741
	Natural variant	173	1	K → E in CMD1. Ref.12		VAR_063647
	Natural variant	354 – 356	3	Missing in CMD1.		VAR_003742

Sequences

	Sequence		Length	Mass (Da)
	P48436 [UniParc]. Last modified February 1, 1996. Version 1. Checksum: 9289CFBB8D6631A2	FASTA	509	56,137
	10 20 30 40 50 60 MNLLDPFMKM TDEQEKGLSG APSPTMSEDS AGSPCPSGSG SDTENTRPQE NTFPKGEPDL 70 80 90 100 110 120 KKESEEDKFP VCIREAVSQV LKGYDWTLVP MPVRVNGSSK NKPHVKRPMN AFMVWAQAAR 130 140 150 160 170 180 RKLADQYPHL HNAELSKTLG KLWRLLNESE KRPFVEEAER LRVQHKKDHP DYKYQPRRRK 190 200 210 220 230 240 SVKNGQAEAE EATEQTHISP NAIFKALQAD SPHSSSGMSE VHSPGEHSGQ SQGPPTPPTT 250 260 270 280 290 300 PKTDVQPGKA DLKREGRPLP EGGRQPPIDF RDVDIGELSS DVISNIETFD VNEFDQYLPP 310 320 330 340 350 360 NGHPGVPATH GQVTYTGSYG ISSTAATPAS AGHVWMSKQQ APPPPPQQPP QAPPAPQAPP 370 380 390 400 410 420 QPQAAPPQQP AAPPQQPQAH TLTTLSSEPG QSQRTHIKTE QLSPSHYSEQ QQHSPQQIAY 430 440 450 460 470 480 SPFNLPHYSP SYPPITRSQY DYTDHQNSSS YYSHAAGQGT GLYSTFTYMN PAQRPMYTPI 490 500 ADTSGVPSIP QTHSPQHWEQ PVYTQLTRP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene." Foster J.W., Dominguez-Steglich M.A., Guioli S., Kowk G., Weller P.A., Stevanovic M., Weissenbach J., Mansour S., Young I.D., Goodfellow P.N., Schafer A.J. Nature 372:525-530(1994) [PubMed: 7990924] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Testis.
[2]	"Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9." Wagner T., Wirth J., Meyer J., Zabel B., Held M., Zimmer J., Pasantes J., Bricarelli F.D., Keutel J., Hustert E., Wolf U., Tommerup N., Schempp W., Scherer G. Cell 79:1111-1120(1994) [PubMed: 8001137] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye and PNS.
[6]	"A SOX9 duplication and familial 46,XX developmental testicular disorder." Cox J.J., Willatt L., Homfray T., Woods C.G. N. Engl. J. Med. 364:91-93(2011) [PubMed: 21208124] [Abstract] Cited for: INVOLVEMENT IN SRXX2.
[7]	"Mutations in SRY and SOX9: testis-determining genes." Cameron F.J., Sinclair A.H. Hum. Mutat. 9:388-395(1997) [PubMed: 9143916] [Abstract] Cited for: REVIEW ON VARIANTS.
[8]	"Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal." Kwok C., Weller P.A., Guioli S., Foster J.W., Mansour S., Zuffardi O., Punnett H.H., Dominguez-Steglich M.A., Brook J.D., Young I.D., Goodfellow P.N., Schafer A.J. Am. J. Hum. Genet. 57:1028-1036(1995) [PubMed: 7485151] [Abstract] Cited for: VARIANTS CMD1 LEU-112 AND VAL-119.
[9]	"Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations." Meyer J., Suedbeck P., Held M., Wagner T., Schmitz M.L., Bricarelli F.D., Eggermont E., Friedrich U., Haas O.A., Kobelt A., Leroy J.G., van Maldergem L., Michel E., Mitulla B., Pfeiffer R.A., Schinzel A., Schmidt H., Scherer G. Hum. Mol. Genet. 6:91-98(1997) [PubMed: 9002675] [Abstract] Cited for: VARIANTS CMD1 LEU-108; ARG-143; PRO-152 AND ARG-170.
[10]	"Novel missense mutation in the HMG box of SOX9 gene in a Japanese XY male resulted in campomelic dysplasia and severe defect in masculinization." Goji K., Nishijima E., Tsugawa C., Nishio H., Pokharel R.K., Matsuo M. Hum. Mutat. Suppl. 1:S114-S116(1998) [PubMed: 9452059] [Abstract] Cited for: VARIANT CMD1 SER-112.
[11]	"Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia." McDowall S., Argentaro A., Ranganathan S., Weller P., Mertin S., Mansour S., Tolmie J., Harley V. J. Biol. Chem. 274:24023-24030(1999) [PubMed: 10446171] [Abstract] Cited for: VARIANTS CMD1 LEU-112; VAL-119; TYR-165 AND ARG-170, 3D-STRUCTURE MODELING.
[12]	"Acampomelic campomelic dysplasia with SOX9 mutation." Thong M.-K., Scherer G., Kozlowski K., Haan E., Morris L. Am. J. Med. Genet. 93:421-425(2000) [PubMed: 10951468] [Abstract] Cited for: VARIANT CMD1 GLU-173.
[13]	"Acampomelic campomelic syndrome." Moog U., Jansen N.J., Scherer G., Schrander-Stumpel C.T. Am. J. Med. Genet. 104:239-245(2001) [PubMed: 11754051] [Abstract] Cited for: VARIANT CMD1 TYR-165.
[14]	"Compound effects of point mutations causing campomelic dysplasia/autosomal sex reversal upon SOX9 structure, nuclear transport, DNA binding, and transcriptional activation." Preiss S., Argentaro A., Clayton A., John A., Jans D.A., Ogata T., Nagai T., Barroso I., Schafer A.J., Harley V.R. J. Biol. Chem. 276:27864-27872(2001) [PubMed: 11323423] [Abstract] Cited for: VARIANTS CMD1 LEU-154 AND THR-158, CHARACTERIZATION OF VARIANTS CMD1 LEU-154 AND THR-158.
[15]	"Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia." Sock E., Pagon R.A., Keymolen K., Lissens W., Wegner M., Scherer G. Hum. Mol. Genet. 12:1439-1447(2003) [PubMed: 12783851] [Abstract] Cited for: VARIANT CMD1 GLU-76.
[16]	"Mutation analysis of SOX9 and single copy number variant analysis of the upstream region in eight patients with campomelic dysplasia and acampomelic campomelic dysplasia." Wada Y., Nishimura G., Nagai T., Sawai H., Yoshikata M., Miyagawa S., Hanita T., Sato S., Hasegawa T., Ishikawa S., Ogata T. Am. J. Med. Genet. A 149:2882-2885(2009) [PubMed: 19921652] [Abstract] Cited for: VARIANTS CMD1 THR-113 AND LEU-170.
[17]	"Heterozygous SOX9 mutations allowing for residual DNA-binding and transcriptional activation lead to the acampomelic variant of campomelic dysplasia." Staffler A., Hammel M., Wahlbuhl M., Bidlingmaier C., Flemmer A.W., Pagel P., Nicolai T., Wegner M., Holzinger A. Hum. Mutat. 31:E1436-E1444(2010) [PubMed: 20513132] [Abstract] Cited for: VARIANTS CMD1 VAL-113 AND GLN-165, CHARACTERIZATION OF VARIANTS CMD1 VAL-113 AND GLN-165.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z46629 mRNA. Translation: CAA86598.1.
S74506, S74504, S74505 Genomic DNA. Translation: AAB32870.1.
BT006875 mRNA. Translation: AAP35521.1.
CH471099 Genomic DNA. Translation: EAW89102.1.
BC007951 mRNA. Translation: AAH07951.1.
BC056420 mRNA. Translation: AAH56420.1.

IPI

IPI00009713.

PIR

A55204.

RefSeq

NP_000337.1. NM_000346.3.

UniGene

Hs.647409.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1S9M	model	-	A	101-177	[»]
1SX9	model	-	A	101-177	[»]

ProteinModelPortal

P48436.

SMR

P48436. Positions 105-178.

ModBase

Search...

Protein-protein interaction databases

IntAct

P48436. 1 interaction.

STRING

P48436.

PTM databases

PhosphoSite

P48436.

Polymorphism databases

DMDM

1351096.

Proteomic databases

PRIDE

P48436.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000245479; ENSP00000245479; ENSG00000125398.

GeneID

6662.

KEGG

hsa:6662.

UCSC

uc002jiw.1. human.

Organism-specific databases

CTD

6662.

GeneCards

GC17P070117.

H-InvDB

HIX0014127.

HGNC

HGNC:11204. SOX9.

HPA

CAB022456.
HPA001758.

MIM

114290. phenotype.
278850. phenotype.
608160. gene.

neXtProt

NX_P48436.

Orphanet

140. Campomelic dysplasia.

PharmGKB

PA36041.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG04276.

GeneTree

ENSGT00600000084111.

HOGENOM

HBG447471.

HOVERGEN

HBG002061.

InParanoid

P48436.

OMA

GAGHVWM.

OrthoDB

EOG4TXBRZ.

PhylomeDB

P48436.

Gene expression databases

ArrayExpress

P48436.

Bgee

P48436.

CleanEx

HS_SOX9.

Genevestigator

P48436.

GermOnline

ENSG00000125398. Homo sapiens.

Family and domain databases

InterPro

IPR000910. HMG_HMG1/HMG2.
IPR009071. HMG_superfamily.
IPR022151. Sox_N.
[Graphical view]

Gene3D

G3DSA:1.10.30.10. HMG-box. 1 hit.

KO

K09270.

Pfam

PF00505. HMG_box. 1 hit.
PF12444. Sox_N. 1 hit.
[Graphical view]

SMART

SM00398. HMG. 1 hit.
[Graphical view]

SUPFAM

SSF47095. HMG-box. 1 hit.

PROSITE

PS50118. HMG_BOX_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

25973.

SOURCE

Search...

Entry information

Entry name

SOX9_HUMAN

Accession

Primary (citable) accession number: P48436
Secondary accession number(s): Q53Y80

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	February 1, 1996
Last modified:	January 25, 2012
This is version 123 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.