Gene Gene information from NCBI Gene database.
Entrez ID 6473
Gene name SHOX homeobox
Gene symbol SHOX
Synonyms (NCBI Gene)
GCFXPHOGSHOX1SHOXYSS
Chromosome X|Y
Chromosome location X;Y
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 pati
SNPs SNP information provided by dbSNP.
23
SNP ID Visualize variation Clinical significance Consequence
rs111549748 G>C Conflicting-interpretations-of-pathogenicity 5 prime UTR variant
rs113313554 C>A,T Conflicting-interpretations-of-pathogenicity 5 prime UTR variant
rs137852552 C>A,T Pathogenic Synonymous variant, coding sequence variant, stop gained
rs137852553 C>G,T Pathogenic Synonymous variant, coding sequence variant, stop gained
rs137852554 C>G Pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
353
miRTarBase ID miRNA Experiments Reference
MIRT666377 hsa-miR-6808-5p HITS-CLIP 23824327
MIRT666376 hsa-miR-6893-5p HITS-CLIP 23824327
MIRT666375 hsa-miR-940 HITS-CLIP 23824327
MIRT666374 hsa-miR-3929 HITS-CLIP 23824327
MIRT666373 hsa-miR-4419b HITS-CLIP 23824327
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
HOXA9 Unknown 23028966
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
19
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IEA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific ISA
GO:0001228 Function DNA-binding transcription activator activity, RNA polymerase II-specific IDA 11751690
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
312865 N/A HGNC
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O15266
Protein name Short stature homeobox protein (Pseudoautosomal homeobox-containing osteogenic protein) (Short stature homeobox-containing protein)
Protein function Controls fundamental aspects of growth and development.
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00046 Homeodomain 118 174 Homeodomain Domain
PF03826 OAR 271 288 OAR motif Motif
Tissue specificity 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
Sequence
MEELTAFVSKSFDQKSKDGNGGGGGGGGKKDSITYREVLESGLARSRELGTSDSSLQDIT
EGGGHCPVHLFKDHVDNDKEKLKEFGTARVAEGIYECKEKREDVKSEDEDGQTKLKQRRS
RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRK
QENQMH
KGVILGTANHLDACRVAPYVNMGALRMPFQQVQAQLQLEGVAHAHPHLHPHLAAHAPYLM
FPPPPFGLPIASLAESASAAAVVAAAAKSNSKNSSIADLRLKARKHAEALGL
Sequence length 292
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
10
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Connective tissue disorder Likely pathogenic rs2124165604 RCV002278796
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Langer mesomelic dysplasia syndrome Likely pathogenic; Pathogenic rs137852557, rs757845999, rs1569493663, rs2522102022, rs397514461 RCV000010555
RCV000010557
RCV000010558
RCV003985970
RCV000022888
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leri-Weill dyschondrosteosis Pathogenic; Likely pathogenic rs746801054, rs2124154821, rs1425206026, rs757391565, rs765251991, rs2052925859, rs752208304, rs1569495224, rs2522102328, rs137852552, rs137852553, rs137852554, rs137852555, rs2522084197, rs137852556
View all (9 more)
RCV002246450
RCV001808132
RCV002246699
RCV002246700
RCV002246702
View all (19 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nonpapillary renal cell carcinoma Likely pathogenic rs2522131120 RCV005933649
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
CONNECTIVE TISSUE DISEASES Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Gastric cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Achondroplasia Achondroplasia BEFREE 12476453, 22946287
★☆☆☆☆
Found in Text Mining only
Acquired cubitus valgus Cubitus valgus BEFREE 17182655
★☆☆☆☆
Found in Text Mining only
Acquired cubitus valgus Cubitus valgus HPO_DG
★☆☆☆☆
Found in Text Mining only
Aromatase deficiency Aromatase Deficiency BEFREE 10946905
★☆☆☆☆
Found in Text Mining only
Becker Muscular Dystrophy Becker Muscular Dystrophy BEFREE 18059093
★☆☆☆☆
Found in Text Mining only
Bone Diseases Bone disease Pubtator 30626445 Associate
★☆☆☆☆
Found in Text Mining only
Brachydactyly Brachydactyly HPO_DG
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate BEFREE 11889216
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate HPO_DG
★☆☆☆☆
Found in Text Mining only
CATSHL syndrome Catshl syndrome Pubtator 19016538 Stimulate
★☆☆☆☆
Found in Text Mining only