OMIA:000081-9796 : Atlanto occipital fusion in Equus caballus (horse)

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

Possibly relevant human trait(s) and/or gene(s) (MIM number): 142980 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2017

Cross-species summary: Also called occipitoatlantoaxial malformation (OAAM)

Molecular basis: Bordbari et al. (2017): "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3. A genotyping assay revealed that both parents of [the affected horse] OAAM1 were heterozygous for the deletion. Additional genotyping identified two of 162 heterozygote Arabians, and the deletion was not present in 371 horses of other breeds"

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

Breed: Arab (Horse) (VBO_0000905).
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
HOXD3 homeobox D3 Equus caballus 18 NC_009161.3 (54654561..54667180) HOXD3 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
691 Arab (Horse) Atlanto occipital fusion HOXD3 deletion, gross (>20) Naturally occurring variant 18 "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3." 2017 28111759

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2017). OMIA:000081-9796: 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.

2017 Bordbari, M.H., Penedo, M.C., Aleman, M., Valberg, S.J., Mickelson, J., Finno, C.J. :
Deletion of 2.7 kb near HOXD3 in an Arabian horse with occipitoatlantoaxial malformation. Anim Genet , 2017. Pubmed reference: 28111759. DOI: 10.1111/age.12531.
2007 Bell, S., Detweiler, D., Benak, J., Pusterla, N. :
What is your diagnosis? Occipitoatlantoaxial malformation. J Am Vet Med Assoc 231:1033-4, 2007. Pubmed reference: 17916027. DOI: 10.2460/javma.231.7.1033.
1989 de Lahunta, A., Hatfield, C., Dietz, A. :
Occipitoatlantoaxial malformation with duplication of the atlas and axis in a half Arabian foal. Cornell Vet 79:185-93, 1989. Pubmed reference: 2924582.
1986 Watson, A.G., Mayhew, I.G. :
Familial congenital occipitoatlantoaxial malformation (OAAM) in the Arabian horse. Spine (Phila Pa 1976) 11:334-9, 1986. Pubmed reference: 3750063.
1985 Wilson, W.D., Hughes, S.J., Ghoshal, N.G., McNeel, S.V. :
Occipitoatlantoaxial malformation in two non-Arabian horses. J Am Vet Med Assoc 187:36-40, 1985. Pubmed reference: 4019299.
1978 Mayhew, I.G., Watson, A.G., Heissan, J.A. :
Congenital occipitoatlantoaxial malformations in the horse. Equine Vet J 10:103-13, 1978. Pubmed reference: 565704.
1974 Leipoid, H.W., Brandt, G.W., Guffy, M., Blauch, B. :
Congenital atlanto-occipital fusion in a foal. Vet Med Small Anim Clin 69:1312-6, 1974. Pubmed reference: 4496765.

Edit History

  • Created by Frank Nicholas on 06 Sep 2005
  • Changed by Frank Nicholas on 07 Oct 2011
  • Changed by Frank Nicholas on 26 Jan 2017