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    SOX3 SRY-box transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 6658, updated on 9-Dec-2024

    Summary

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    Official Symbol
    SOX3provided by HGNC
    Official Full Name
    SRY-box transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:11199
    See related
    Ensembl:ENSG00000134595 MIM:313430; AllianceGenome:HGNC:11199
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PHP; GHDX; MRGH; PHPX; SOXB
    Summary
    This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. Mutations in this gene have been associated with X-linked cognitive disability with growth hormone deficiency. [provided by RefSeq, Jul 2008]
    Orthologs
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    Genomic context

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    See SOX3 in Genome Data Viewer
    Location:
    Xq27.1
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (140502985..140505069, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (138814872..138816956, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (139585150..139587234, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene U7 small nuclear RNA Neighboring gene ribosomal protein S17 pseudogene 17 Neighboring gene SOX3 promoter region Neighboring gene uncharacterized LOC105373344 Neighboring gene NANOG hESC enhancer GRCh37_chrX:139608152-139608653 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:139655621-139655814 Neighboring gene uncharacterized LOC101928833

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A novel mutation (c. 341A>G) in the SRY gene in a 46,XY female patient with gonadal dysgenesis. Helszer Z, et al. Gene, 2013 Sep 10. PMID 23624391
    2. A complex phenotype in a family with a pathogenic SOX3 missense variant. Jelsig AM, et al. Eur J Med Genet, 2018 Mar. PMID 29175558
    3. Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells. Topalovic V, et al. PLoS One, 2017. PMID 28886103, Free PMC Article
    4. Study of six patients with complete F9 deletion characterized by cytogenetic microarray: role of the SOX3 gene in intellectual disability. Jourdy Y, et al. J Thromb Haemost, 2016 Oct. PMID 27477789
    5. Marked phenotypic variable expression among brothers with duplication of Xq27.1 involving the SOX3 gene. Rosolowsky ET, et al. J Pediatr Endocrinol Metab, 2020 Mar 26. PMID 26352083

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Do SOD2 and SOD3 gene polymorphisms impact the oral health-related quality of life in Para athletes?
      Title: Do SOD2 and SOD3 gene polymorphisms impact the oral health-related quality of life in Para athletes?
    2. Clinical Correlation of Transcription Factor SOX3 in Cancer: Unveiling Its Role in Tumorigenesis.
      Title: Clinical Correlation of Transcription Factor SOX3 in Cancer: Unveiling Its Role in Tumorigenesis.
    3. ROR2 deficit may induce the tetralogy of Fallot via down-regulating of beta-catenin/SOX3/HSPA6 in vitro and in vivo.
      Title: ROR2 deficit may induce the tetralogy of Fallot via down-regulating of β-catenin/SOX3/HSPA6 in vitro and in vivo.
    4. A complex structural variant near SOX3 causes X-linked split-hand/foot malformation.
      Title: A complex structural variant near SOX3 causes X-linked split-hand/foot malformation.
    5. Transcription factor SOX3 upregulated pro-apoptotic genes expression in human breast cancer.
      Title: Transcription factor SOX3 upregulated pro-apoptotic genes expression in human breast cancer.
    6. A SOX3 duplication and lumbosacral spina bifida in three generations.
      Title: A SOX3 duplication and lumbosacral spina bifida in three generations.
    7. LINC00662 Promotes Proliferation and Invasion and Inhibits Apoptosis of Glioma Cells Through miR-483-3p/SOX3 Axis.
      Title: LINC00662 Promotes Proliferation and Invasion and Inhibits Apoptosis of Glioma Cells Through miR-483-3p/SOX3 Axis.
    8. Allelic Variants in Established Hypopituitarism Genes Expand Our Knowledge of the Phenotypic Spectrum.
      Title: Allelic Variants in Established Hypopituitarism Genes Expand Our Knowledge of the Phenotypic Spectrum.
    9. Serum proteome profiling reveals SOX3 as a candidate prognostic marker for gastric cancer.
      Title: Serum proteome profiling reveals SOX3 as a candidate prognostic marker for gastric cancer.
    10. Marked phenotypic variable expression among brothers with duplication of Xq27.1 involving the SOX3 gene.
      Title: Marked phenotypic variable expression among brothers with duplication of Xq27.1 involving the SOX3 gene.
    Submit: New GeneRIF Correction See all GeneRIFs (49)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, X-linked, with panhypopituitarism
    MedGen: C2678223 OMIM: 300123 GeneReviews: Not available
    		Compare labs
    Panhypopituitarism, X-linked
    MedGen: C0342376 OMIM: 312000 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    Some evidence for dosage pathogenicity (Last evaluated 2023-01-10)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    No evidence available (Last evaluated 2023-01-10)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in central nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in face development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in hypothalamus development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pituitary gland development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sensory organ development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sex determination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor SOX-3
    Names
    SRY (sex determining region Y)-box 3
    SRY-box 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009387.1 RefSeqGene

      Range
      4992..7076
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005634.3 → NP_005625.2  transcription factor SOX-3

      See identical proteins and their annotated locations for NP_005625.2

      Status: REVIEWED

      Source sequence(s)
      AL121875
      Consensus CDS
      CCDS14669.1
      UniProtKB/Swiss-Prot
      P35714, P41225, Q5JWI3, Q9NP49
      Related
      ENSP00000359567.2, ENST00000370536.5
      Conserved Domains (2) summary
      cd01388
      Location:138 → 209
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
      pfam12336
      Location:208 → 302
      SOXp; SOX transcription factor

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      140502985..140505069 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      138814872..138816956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P41225.2 GenPept UniProtKB/Swiss-Prot:P41225

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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