AtlasGene
SHOX
SHOX homeobox
- HGNC 10853↗(opens in a new tab)
- Ensembl gene ENSG00000185960↗(opens in a new tab)
- NCBI Gene 6473↗(opens in a new tab)
Summary
- Cytogenetic location
- Xp22.33 and Yp11.32
- Coordinates
- Chromosome X: 630,791–651,584 (GRCh38)
- Exons
- 5 exons across 20.8 kb
- Protein
- 292 amino acids
- Also known as
- PHOG, GCFX, SS, SHOXY, SHOX1
- MANE Select transcript
- ENST00000686671.1NM_000451.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/shox.json"
page <- fromJSON(url)
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SHOX Deficiency (Leri-Weill and Langer Dysplasia)
- Leri-Weill dyschondrosteosis
Short stature with shortened forearms and lower legs and a characteristic wrist deformity (Madelung deformity), caused by loss of one copy of SHOX or its regulatory regions.
- 4 GenCC submitters rate it definitive or strong
▶Actionability
Growth hormone treatment is approved for children with short stature due to SHOX deficiency.
- Langer mesomelic dysplasia
A more severe form of SHOX deficiency, with marked shortening of the forearms and lower legs, caused by loss of both copies of SHOX.
- 3 GenCC submitters rate it definitive or strong
How SHOX is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 7.9 kb of the gene's 20.8 kb; 879 of those bases code for the protein.
Sequencing SHOX
10Moderate
How hard SHOX is to sequence with short reads, out of 100Each bar is the share of SHOX's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.14%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.25%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.9.8%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
24
positions in SHOX where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 20.8 kb of SHOX, introns included, not only the 7.9 kb of exons.
Traits linked to SHOX
The Human Phenotype Ontology lists these as features of the rare conditions SHOX can cause. Each trait's page lists the other genes linked to it.
Abnormality of limbs
- Increased carrying angle
- Madelung deformity
- Mesomelic arm shortening
- Rhizomelic arm shortening
- Abnormal humerus morphology
- Abnormal morphology of the radius
- Abnormal morphology of ulna
- Abnormal wrist bones
Show 40 more traits
- Abnormality of the shankbone
- Abnormality of the thighbone
- Abnormality of the wide portion of a long bone
- Absent kneecap
- Absent/small calf bone
- Bowed shankbone
- Bowing of outer large bone of the forearm
- Bowing of the long bones
- Curvature of little finger
- Curving of inner forearm bone
- Disproportionately short middle portion of limb
- Dorsal subluxation of ulna
- Finger bends toward pinky
- Forearm undergrowth
- Knock knees
- Limited wrist movement
- Lower limb undergrowth
- Mesomelic/rhizomelic limb shortening
- Outward bow-leggedness
- Outward turned elbows
- Short fingers or toes
- Short foot
- Short neck of thighbone
- Short shinbone
- Smaller or shorter than typical limbs
- Thickening of shaft or central part of long bones
- Ulnar radial head dislocation
- Underdeveloped inner large forearm bone
- Underdeveloped outer large forearm bone
- Elbow dislocation
- Abnormal neck of thigh bone
- Abnormal shape of long bones of hand
- Abnormality of the long bone of foot
- Broad ulna
- Coxa valga
- Limited elbow movement
- Short calf bone
- Short toe
- Shortened 4th long bone of hand
- Small to absent calf bone
Abnormality of the musculoskeletal system
- Abnormal shape of end part of bone
- Abnormal shape of pelvic girdle bone
- Abnormality of the hip bone
- Cone-shaped end part of bone
- Formation of new noncancerous bone on top of existing bone
- Increased skeletal muscle cells
- Joint stiffness
- Scoliosis
Show 2 more traits
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-e609d43e.
Cite this page
Dante Labs. (n.d.). SHOX gene: SHOX homeobox. Retrieved 18 October 2026, from https://dantelabs.com/genes/shox
Dante Labs. SHOX gene: SHOX homeobox [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/shox
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