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Aliases for SHOX Gene

Aliases for SHOX Gene

  • Short Stature Homeobox 2 3 5
  • Pseudoautosomal Homeobox-Containing Osteogenic Protein 3 4
  • PHOG 3 4
  • Short Stature Homeobox-Containing Protein 4
  • Growth Control Factor, X-Linked 3
  • Short Stature Homeobox Protein 3
  • SHOXY 3
  • GCFX 3
  • SS 3

External Ids for SHOX Gene

Previous GeneCards Identifiers for SHOX Gene

  • GC0XP000427
  • GC0YU900006
  • GC0XP000527
  • GC0YP000555
  • GC0XP000585

Summaries for SHOX Gene

Entrez Gene Summary for SHOX Gene

  • 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]

GeneCards Summary for SHOX Gene

SHOX (Short Stature Homeobox) is a Protein Coding gene. Diseases associated with SHOX include Leri-Weill Dyschondrosteosis and Langer Mesomelic Dysplasia. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and sequence-specific DNA binding. An important paralog of this gene is SHOX2.

UniProtKB/Swiss-Prot for SHOX Gene

  • Controls fundamental aspects of growth and development.

Gene Wiki entry for SHOX Gene

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

Genomics for SHOX Gene

Regulatory Elements for SHOX Gene

Genomic Location for SHOX Gene

624,344 bp from pter
659,411 bp from pter
35,068 bases
Plus strand

Genomic View for SHOX Gene

Genes around SHOX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SHOX Gene

Proteins for SHOX Gene

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

    Protein Symbol:
    Recommended name:
    Short stature homeobox protein
    Protein Accession:
    Secondary Accessions:
    • O00412
    • O00413
    • O15267

    Protein attributes for SHOX Gene

    292 amino acids
    Molecular mass:
    32236 Da
    Quaternary structure:
    No Data Available
    • The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.

    Alternative splice isoforms for SHOX Gene


neXtProt entry for SHOX Gene

Post-translational modifications for SHOX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SHOX Gene

No data available for DME Specific Peptides for SHOX Gene

Domains & Families for SHOX Gene

Suggested Antigen Peptide Sequences for SHOX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the paired homeobox family. Bicoid subfamily.
  • Belongs to the paired homeobox family. Bicoid subfamily.
genes like me logo Genes that share domains with SHOX: view

Function for SHOX Gene

Molecular function for SHOX Gene

GENATLAS Biochemistry:
short stature homeo box-containing gene,with two alternatively spliced forms SHOXa widely expressed,and SHOXb predominantly found in bone marrow,fibroblast,homolog to murine OG-12a,OG-12b
UniProtKB/Swiss-Prot Function:
Controls fundamental aspects of growth and development.
UniProtKB/Swiss-Prot Induction:
By retinoic acid and phorbol-12-myristate 13-acetate (PMA).

Gene Ontology (GO) - Molecular Function for SHOX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IMP 11751690
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 9259282
GO:0005515 protein binding IPI 21262861
GO:0043565 sequence-specific DNA binding IMP 11751690
genes like me logo Genes that share ontologies with SHOX: view
genes like me logo Genes that share phenotypes with SHOX: view

Human Phenotype Ontology for SHOX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SHOX Gene

Localization for SHOX Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHOX 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 SHOX gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for SHOX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with SHOX: view

Pathways & Interactions for SHOX Gene

No Data Available

SIGNOR curated interactions for SHOX Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SHOX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9590292
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS 9259282
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SHOX: view

No data available for Pathways by source for SHOX Gene

Drugs & Compounds for SHOX Gene

(1) Drugs for SHOX Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for SHOX Gene - From: Novoseek

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

Transcripts for SHOX Gene

mRNA/cDNA for SHOX Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SHOX Gene

Short stature homeobox:
Representative Sequences:

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for SHOX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SHOX Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Adipose - Subcutaneous (x17.9), Muscle - Skeletal (x7.1), Artery - Tibial (x6.8), and Skin - Sun Exposed (Lower leg) (x4.2).

Protein differential expression in normal tissues from HIPED for SHOX Gene

This gene is overexpressed in Adipocyte (69.0).

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

Protein tissue co-expression partners for SHOX Gene

NURSA nuclear receptor signaling pathways regulating expression of SHOX Gene:


SOURCE GeneReport for Unigene cluster for SHOX Gene:


mRNA Expression by UniProt/SwissProt for SHOX Gene:

Tissue specificity: SHOXA is expressed in skeletal muscle, placenta, pancreas, heart and bone marrow fibroblast and SHOXB is highly expressed in bone marrow fibroblast followed by kidney and skeletal muscle. SHOXB is not expressed in brain, kidney, liver and lung. Highly expressed in osteogenic cells.

Evidence on tissue expression from TISSUES for SHOX Gene

  • Muscle(4)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • chin
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SHOX: view

Primer Products

Orthologs for SHOX Gene

This gene was present in the common ancestor of animals.

Orthologs for SHOX Gene

Organism Taxonomy Gene Similarity Type Details
(Monodelphis domestica)
Mammalia SHOX 35
  • 93 (a)
(Canis familiaris)
Mammalia SHOX 34 35
  • 90.26 (n)
(Bos Taurus)
Mammalia SHOX 34 35
  • 87.67 (n)
(Ornithorhynchus anatinus)
Mammalia SHOX 35
  • 71 (a)
(Gallus gallus)
Aves SHOX 34 35
  • 84.77 (n)
(Anolis carolinensis)
Reptilia SHOX 35
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shox 34
  • 75.09 (n)
(Danio rerio)
Actinopterygii shox 34 35
  • 75.85 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34367 35
  • 32 (a)
(Caenorhabditis elegans)
Secernentea alr-1 35
  • 18 (a)
Species where no ortholog for SHOX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 SHOX Gene

Gene Tree for SHOX (if available)
Gene Tree for SHOX (if available)

Paralogs for SHOX Gene

Paralogs for SHOX Gene

(2) SIMAP similar genes for SHOX Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SHOX: view

Variants for SHOX Gene

Sequence variations from dbSNP and Humsavar for SHOX Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs137852554 Pathogenic, Leri-Weill dyschondrosteosis (LWD) [MIM:127300] 634,734(+) ACGAG(C/G)TCGAG reference, missense
rs137852555 Pathogenic, Leri-Weill dyschondrosteosis (LWD) [MIM:127300] 634,798(+) CCAGC(G/T)CCTGG reference, missense
rs137852556 Pathogenic, Leri-Weill dyschondrosteosis (LWD) [MIM:127300] 640,851(+) AGTGC(C/T)GCAAA reference, missense
rs137852557 Pathogenic, Langer mesomelic dysplasia (LMD) [MIM:249700] 640,836(+) AGAAC(C/T)GGAGA reference, missense
rs1057518701 Pathogenic 640,879(+) TAAAG(A/G)TGGGT splice-donor-variant

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

Variant ID Type Subtype PubMed ID
dgv1288e201 CNV deletion 23290073
dgv4555e59 CNV duplication 20981092
esv2664240 CNV deletion 23128226
esv2676175 CNV deletion 23128226
esv2739493 CNV deletion 23290073
esv2739494 CNV deletion 23290073
esv2739495 CNV deletion 23290073
esv2739497 CNV deletion 23290073
esv2739498 CNV deletion 23290073
esv2739499 CNV deletion 23290073
esv2739500 CNV deletion 23290073
esv2739501 CNV deletion 23290073
esv2739502 CNV deletion 23290073
esv2739503 CNV deletion 23290073
esv2739504 CNV deletion 23290073
esv2739505 CNV deletion 23290073
esv2739506 CNV deletion 23290073
esv2739508 CNV deletion 23290073
esv2743216 CNV deletion 23290073
esv3558431 CNV deletion 23714750
nsv10004 CNV loss 18304495
nsv1140086 CNV duplication 24896259
nsv507942 OTHER sequence alteration 20534489
nsv9923 CNV loss 18304495

Variation tolerance for SHOX Gene

Residual Variation Intolerance Score: 26.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.46; 10.08% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SHOX Gene

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

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

Disorders for SHOX Gene

MalaCards: The human disease database

(22) MalaCards diseases for SHOX Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
leri-weill dyschondrosteosis
  • leri weill dyschondrosteosis
langer mesomelic dysplasia
  • dyschondrosteosis, homozygous
short stature, idiopathic familial
  • short stature, idiopathic, x-linked
langer mesomelic dwarfism
shox-related haploinsufficiency disorders
- elite association - COSMIC cancer census association via MalaCards
Search SHOX in MalaCards View complete list of genes associated with diseases


  • Langer mesomelic dysplasia (LMD) [MIM:249700]: Autosomal recessive rare skeletal dysplasia characterized by severe short stature owing to shortening and maldevelopment of the mesomelic and rhizomelic segments of the limbs. Associated malformations are rarely reported and intellect is normal in all affected subjects reported to date. {ECO:0000269 PubMed:11889214}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Leri-Weill dyschondrosteosis (LWD) [MIM:127300]: Dominantly inherited skeletal dysplasia characterized by moderate short stature predominantly because of short mesomelic limb segments. It is often associated with the Madelung deformity of the wrist, comprising bowing of the radius and dorsal dislocation of the distal ulna. {ECO:0000269 PubMed:11030412, ECO:0000269 PubMed:11403039}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Short stature, idiopathic, X-linked (ISS) [MIM:300582]: A condition defined by a standing height more than 2 standard deviations below the mean (or below the 2.5 percentile) for sex and chronological age, compared with a well-nourished, genetically relevant population, in the absence of specific causative disorders. {ECO:0000269 PubMed:9140395}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SHOX

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SHOX: view

No data available for Genatlas for SHOX Gene

Publications for SHOX Gene

  1. Pseudoautosomal deletions encompassing a novel homeobox gene cause growth failure in idiopathic short stature and Turner syndrome. (PMID: 9140395) Rao E. … Rappold G.A. (Nat. Genet. 1997) 2 3 4 22 64
  2. PHOG, a candidate gene for involvement in the short stature of Turner syndrome. (PMID: 9259282) Ellison J.W. … Chiong W. (Hum. Mol. Genet. 1997) 2 3 4 22 64
  3. Enhancer deletions of the SHOX gene as a frequent cause of short stature: the essential role of a 250 kb downstream regulatory domain. (PMID: 19578035) Chen J. … Rappold G. (J. Med. Genet. 2009) 3 22 46 64
  4. SHOX nullizygosity and haploinsufficiency in a Japanese family: implication for the development of Turner skeletal features. (PMID: 11889214) Ogata T. … Hattori T. (J. Clin. Endocrinol. Metab. 2002) 3 4 22 64
  5. Deletions of the homeobox gene SHOX (short stature homeobox) are an important cause of growth failure in children with short stature. (PMID: 11889216) Rappold G.A. … Ogata T. (J. Clin. Endocrinol. Metab. 2002) 3 22 46 64

Products for SHOX Gene

Sources for SHOX Gene

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