SHOX SHOX homeobox [Homo sapiens (human)] - Gene

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Chromosome Y - NC_000024.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
Title: Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
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.
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.
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.
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.
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

D11S2921 (e-PCR)
- UniSTS:152074

L17705 (e-PCR)
- UniSTS:66091

D8S2279 (e-PCR)
- UniSTS:473907

DXYS28 (e-PCR)
- UniSTS:51293

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

D0S17712 (e-PCR)
- UniSTS:25772

DXYS131 (e-PCR)
- UniSTS:54705

DXYS131 (e-PCR)
- UniSTS:99538

NoName (e-PCR)
- UniSTS:494832

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

NG_009385.2 RefSeqGene

Range

5001..40068

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_710

mRNA and Protein(s)

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
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