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

Gene ID: 6658, updated on 27-Nov-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

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