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    SHOX SHOX homeobox [ Homo sapiens (human) ]

    Gene ID: 6473, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SHOXprovided by HGNC
    Official Full Name
    SHOX homeoboxprovided by HGNC
    Primary source
    HGNC:HGNC:10853
    See related
    Ensembl:ENSG00000185960 Ensembl:ENSG00000292354 MIM:312865; MIM:400020; AllianceGenome:HGNC:10853
    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
    SS; GCFX; PHOG; SHOX1; SHOXY
    Summary
    This gene belongs to the paired homeobox family and is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. Defects in this gene are associated with idiopathic growth retardation and in the short stature phenotype of Turner syndrome patients. This gene is highly conserved across species from mammals to fish to flies. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See SHOX in Genome Data Viewer
    Location:
    X;Y
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (624344..659411)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (624344..659411)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (464175..499150)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (478002..512484)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (585079..620146)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (535079..570146)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene CNE9 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene CNE9 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Imaging of SHOX-associated anomalies. Gahunia HK, et al. Semin Musculoskelet Radiol, 2009 Sep. PMID 19724992
    2. Alteration of DNA binding, dimerization, and nuclear translocation of SHOX homeodomain mutations identified in idiopathic short stature and Leri-Weill dyschondrosteosis. Schneider KU, et al. Hum Mutat, 2005 Jul. PMID 15931687
    3. High incidence of SHOX anomalies in individuals with short stature. Huber C, et al. J Med Genet, 2006 Sep. PMID 16597678, Free PMC Article
    4. Short stature and dysmorphology associated with defects in the SHOX gene. Leka SK, et al. Hormones (Athens), 2006 Apr-Jun. PMID 16807223
    5. Characterization of SHOX deletions in Leri-Weill dyschondrosteosis (LWD) reveals genetic heterogeneity and no recombination hotspots. Benito-Sanz S, et al. Am J Hum Genet, 2006 Aug. PMID 16826534, Free PMC Article

    See all (138) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression levels and DNA methylation profiles of the growth gene SHOX in cartilage tissues and chondrocytes.
      Title: Expression levels and DNA methylation profiles of the growth gene SHOX in cartilage tissues and chondrocytes.
    2. SHOX Variations in Idiopathic Short Stature in North India and a Review of Cases from Asian Countries.
      Title: SHOX Variations in Idiopathic Short Stature in North India and a Review of Cases from Asian Countries.
    3. Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability.
      Title: Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability.
    4. Leri-Weill Dyschondrosteosis Caused by a Leaky Homozygous SHOX Splice-Site Variant.
      Title: Leri-Weill Dyschondrosteosis Caused by a Leaky Homozygous SHOX Splice-Site Variant.
    5. Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
      Title: Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
    6. Adult Height of Patients with SHOX Haploinsufficiency with or without GH Therapy: A Real-World Single-Center Study.
      Title: Adult Height of Patients with SHOX Haploinsufficiency with or without GH Therapy: A Real-World Single-Center Study.
    7. Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Leri-Weill dyschondrosteosis.
      Title: Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis.
    8. Evidence of intrauterine growth restriction and growth hormone deficiency in 49,XXXXY syndrome.
      Title: Evidence of intrauterine growth restriction and growth hormone deficiency in 49,XXXXY syndrome.
    9. Clinical and Genetic Characteristics of 23 Korean Patients with Haploinsufficiency of the Short-stature Homeobox-containing Gene.
      Title: Clinical and Genetic Characteristics of 23 Korean Patients with Haploinsufficiency of the Short-stature Homeobox-containing Gene.
    10. Human Spermatogenesis Tolerates Massive Size Reduction of the Pseudoautosomal Region.
      Title: Human Spermatogenesis Tolerates Massive Size Reduction of the Pseudoautosomal Region.
    Submit: New GeneRIF Correction See all GeneRIFs (122)

    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
    Langer mesomelic dysplasia syndrome
    MedGen: C0432230 OMIM: 249700 GeneReviews: Not available
    		Compare labs
    Leri-Weill dyschondrosteosis
    MedGen: C0265309 OMIM: 127300 GeneReviews: SHOX Deficiency Disorders
    		Compare labs
    SHOX-related short stature
    MedGen: C1845118 OMIM: 300582 GeneReviews: Not available
    		Compare labs

    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 transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor 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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    short stature homeobox protein
    Names
    growth control factor, X-linked
    pseudoautosomal homeobox-containing osteogenic protein
    short stature homeobox

    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_009385.2 RefSeqGene

      Range
      5001..40068
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_710

    mRNA and Protein(s)

    1. NM_000451.4 → NP_000442.1  short stature homeobox protein isoform SHOXa

      See identical proteins and their annotated locations for NP_000442.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (SHOXa).
      Source sequence(s)
      BX004827
      Consensus CDS
      CCDS14107.1
      UniProtKB/Swiss-Prot
      O00412, O00413, O15266, O15267
      UniProtKB/TrEMBL
      Q6IT45
      Related
      ENSP00000508521.1, ENSP00000518640.1, ENST00000686671.1, ENST00000711142.1
      Conserved Domains (2) summary
      pfam00046
      Location:120 → 174
      Homeobox; Homeobox domain
      pfam03826
      Location:272 → 288
      OAR; OAR domain

    2. NM_006883.2 → NP_006874.1  short stature homeobox protein isoform SHOXb

      See identical proteins and their annotated locations for NP_006874.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 3' terminal exon compared to transcript variant 1, and encodes a shorter isoform (SHOXb) with a different C-terminus compared to isoform SHOXa.
      Source sequence(s)
      BX004827
      Consensus CDS
      CCDS14106.1
      UniProtKB/Swiss-Prot
      O15266
      Related
      ENSP00000335505.3, ENSP00000518641.1, ENST00000334060.8, ENST00000711143.1
      Conserved Domains (1) summary
      pfam00046
      Location:120 → 173
      Homeobox; Homeobox domain

    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
      624344..659411
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      624344..659411
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      464175..499150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      478002..512484
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15266.1 GenPept UniProtKB/Swiss-Prot:O15266

    Gene LinkOut

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

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