OMIA:002013-9796 : Skeletal atavism in Equus caballus (horse)

Categories: Skeleton phene (incl. short stature & teeth)

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 312865 (gene) , 249700 (trait) , 127300 (trait) , 300582 (trait)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2016

Cross-species summary: Atavism is a general term for the reappearance of one or more traits that are known to have occurred in remote ancestors, usually from an ancestral species. The term "skeletal atavism" has been applied to horses with abnormal development of ulna and fibula that somewhat resembles the reduction in size of both bones and their fusion to radius and tibula, respectively, in ancestral equids.

History: Affected Shetland ponies were reported in 1958 in the UK, Netherlands and Sweden. This trait is referred to as an atavism because ancestral species appeared to normally exhibit this condition, according to fossil records (reviewed in Rafati et al., 2016). [IT thanks Miranda Slingerland, working under the guidance of Professor Ernie Bailey, for contributions to this entry in April 2022]

Mapping: Rafati et al. (2016) "performed whole genome resequencing of six SA [skeletal atavism] cases and a pool of control horses and use this data to show that skeletal atavism is associated with two, partially overlapping, large deletions on sequence scaffolds not assigned to any chromosome in the EquCab2.0 genome assembly". These "two partially overlapping large deletions [are] in the pseudoautosomal region (PAR) of chromosome X/Y"

Molecular basis: The deletions mentioned in the Mapping section were named Del-1 and Del-2 (Rafati et al., 2016), and the authors reported that "One of the identified deletions removes the entire coding region of the short stature homeobox (SHOX) gene [Del-1] and both deletions remove parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX." The same authors then "sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 160-180 kb [Del-1] and 60-80 kb [Del-2], respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. .... We did not observe any obvious phenotypic difference between Del-1/Del-1 and Del-1/Del-2 individuals."

Genetic engineering: Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing

Clinical features: As reported by Rafati et al. (2016), "Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure, impaired movements, and affected foals are usually euthanized."

Prevalence: When testing a random set of 94 Shetland ponies in Sweden, the allele frequencies of disease associated deletions Del1 and Del2 were 0.0479 and 0.0106, respectively (Rafati et al., 2016)

Breed: Shetland Pony (Horse) (VBO_0001066).
Breeds in which the phene has been documented. For breeds in which a likely causal variant has been documented, see the variant table below

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SHOX short stature homeobox Equus caballus NW_001867655.1 (218906..239005) SHOX Homologene, Ensembl , NCBI gene


By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
686 Shetland Pony (Horse) Skeletal atavism SHOX Del-1 deletion, gross (>20) Naturally occurring variant PAR 160−180 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing the entire coding region of the short stature homeobox (SHOX) gene and parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX 2016 27207956
1455 Shetland Pony (Horse) Skeletal atavism SHOX Del-2 deletion, gross (>20) Naturally occurring variant PAR 60−80 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX 2016 27207956

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:002013-9796: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2016 Rafati, N., Andersson, L.S., Mikko, S., Feng, C., Raudsepp, T., Pettersson, J., Janecka, J., Wattle, O., Ameur, A., Thyreen, G., Eberth, J., Huddleston, J., Malig, M., Bailey, E., Eichler, E.E., Dalin, G., Chowdary, B., Anderssson, L., Lindgren, G., Rubin, C.J. :
Large deletions at the SHOX locus in the pseudoautosomal region are associated with skeletal atavism in Shetland ponies. G3 (Bethesda) 6:2213-2223, 2016. Pubmed reference: 27207956. DOI: 10.1534/g3.116.029645.
2004 Tyson, R., Graham, J.P., Colahan, P.T., Berry, C.R. :
Skeletal atavism in a miniature horse. Vet Radiol Ultrasound 45:315-7, 2004. Pubmed reference: 15373256.
1995 Hall, B.K. :
Atavisms and atavistic mutations. Nat Genet 10:126-7, 1995. Pubmed reference: 7663504. DOI: 10.1038/ng0695-126.
Martens, P. :
Limb deviation in a Shetland pony foal Equine Practice 17:24-26, 1995.
1987 Hermans, W.A., Kersjes, A.W., van der Mey, G.J., Dik, K.J. :
Investigation into the heredity of congenital lateral patellar (sub)luxation in the Shetland pony. Vet Q 9:1-8, 1987. Pubmed reference: 3564314. DOI: 10.1080/01652176.1987.9694070.
1985 Shamis, L.D., Auer, J. :
Complete ulnas and fibulas in a pony foal. J Am Vet Med Assoc 186:802-4, 1985. Pubmed reference: 3997641.
1970 Hermans, W.A. :
A hereditary anomaly in Shetland ponies Netherlands Journal of Veterinary Science 3:55-63, 1970.
1958 Speed, J.G. :
A cause of malformation of the limbs of Shetland ponies with a note on its phylogenic significance British Veterinary Journal 114:18-22, 1958.

Edit History

  • Created by Frank Nicholas on 23 May 2016
  • Changed by Frank Nicholas on 23 May 2016
  • Changed by Frank Nicholas on 24 May 2016
  • Changed by Imke Tammen2 on 30 Apr 2022