OMIA:002013-9796 : Skeletal atavism in Equus caballus
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."
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).
|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|
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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|
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.|
- Changed by Frank Nicholas on 23 May 2016
- Created by Frank Nicholas on 23 May 2016
- Changed by Frank Nicholas on 24 May 2016
- Changed by Imke Tammen2 on 30 Apr 2022