OMIA:001551-9685 : Brachycephaly in Felis catus

In other species: dog , pig , goat

Categories: Craniofacial phene

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 613456 (trait) , 601527 (gene) , 112263 (gene) , 607223 (gene) , 125400 (trait)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal co-dominant

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2016

Species-specific description: As summarised by Lyons et al. (2016), "The Burmese is a cat breed with an extreme brachycephalic phenotype . . .. In the late 1970's, a male Burmese cat in the USA with a more brachycephalic head type became a highly popular sire and his lineage became known as the “Contemporary” Burmese . . . . The head type was found to be heritable, however, offspring from “Contemporary” style mating produced a craniofacial defect in 25% of offspring (Noden and Evans, 1986 and Sponenberg and Graf-Webster, 1986). The abnormality is characterized by agenesis of all derivatives of the medial nasal prominence; lateral duplication of most derivatives of the maxillary process; including the canine teeth and whiskers fields; telencephalic meningoencephalocele; and secondary ocular degeneration . . . . The midline facial defect is autosomal recessive, however, carriers of the mutation are more brachycephalic individuals than wildtype and were positively selected in the breed, thus the trait has also been described as co-dominant. Affected kittens were generally born live and require euthanasia as the condition is incompatible with life. The heterozygous cats became the hallmark phenotype of the “Contemporary” Burmese and the predominant winners at cat shows."

Mapping: Lyons et al. (2016) reported that "Family-based linkage analysis localized the trait to cat chromosome B4".

Markers: Bertolini et al. (2016) identified four ~1Mb regions of homozygosity peculiar to Persian cats (which are characterised by an extreme form of brachycephaly), one of which contains two genes "CHL1 and CNTN6 known to determine face shape modification in humans".

Molecular basis: Lyons et al (2016): "A long-term project that initiated with targeted linkage analysis, and, as domestic cat genomic resources improved, progressed to identity by descent mapping, homozygosity mapping and a genome-wide case-control association study (GWAS) suggests ALX1 as a major gene controlling craniofacial structure and the variant in ALX1 is associated with the Burmese brachycephaly and the craniofacial abnormality". "Sequence analysis identified a 12 bp in frame deletion in ALX1, c.496delCTCTCAGGACTG, which is 100% concordant with the craniofacial defect and not found in cats not related to the Contemporary Burmese."

Breed: Burmese (Cat) (VBO_0100053).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
ALX1 ALX homeobox 1 Felis catus B4 NC_058374.1 (107851193..107872185) ALX1 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
550 Burmese (Cat) Brachycephaly ALX1 deletion, small (<=20) Naturally occurring variant Felis_catus_9.0 B4 g.110088245_110088256del c.497_508del p.(A166_T169del) XM_003989090.4; XP_003989139.1; published as c.496delCTCTCAGGACTG 2016 26610632 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.


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.

2023 Berteselli, G.V., Palestrini, C., Scarpazza, F., Barbieri, S., Prato-Previde, E., Cannas, S. :
Flat-faced or non-flat-faced cats? That is the question. Animals (Basel) 13:206, 2023. Pubmed reference: 36670746 . DOI: 10.3390/ani13020206.
Gleason, H.E., Phillips, H., Fries, R., Keating, S., Hamel, P., McCoy, A. :
Ala vestibuloplasty improves cardiopulmonary and activity-related parameters in brachycephalic cats. Vet Surg 52:575-586, 2023. Pubmed reference: 36882053 . DOI: 10.1111/vsu.13948.
Gündemir, O., Szara, T., Yalin, E.E., Karabagli, M., Mutlu, Z., Yilmaz, O., Büyükünal, S.K., Blagojevic, M., Parés-Casanova, P.M. :
Examination of shape variation of the skull in British Shorthair, Scottish Fold, and Van cats. Animals (Basel) 13:614, 2023. Pubmed reference: 36830403 . DOI: 10.3390/ani13040614.
Gundemir, O., Akcasiz, Z.N., Yilmaz, O., Hadžiomerović, N. :
Radiographic analysis of skull in Van Cats, British Shorthairs and Scottish Folds. Anat Histol Embryol :, 2023. Pubmed reference: 36793158 . DOI: 10.1111/ahe.12909.
2021 Alhaddad, H., Abdi, M., Lyons, L.A. :
Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array. PLoS One 16:e0247092, 2021. Pubmed reference: 33630878 . DOI: 10.1371/journal.pone.0247092.
Geiger, M., Schoenebeck, J.J., Schneider, R.A., Schmidt, M.J., Fischer, M.S., Sánchez-Villagra, M.R. :
Exceptional changes in skeletal anatomy under domestication: The case of brachycephaly. Integr Org Biol 3:obab023, 2021. Pubmed reference: 34409262 . DOI: 10.1093/iob/obab023.
2016 Anon. :
Brachycephaly: an issue for cats as well as dogs. Vet Rec 179:371, 2016. Pubmed reference: 27738208 . DOI: 10.1136/vr.i5507.
Bertolini, F., Gandolfi, B., Kim, E.S., Haase, B., Lyons, L.A., Rothschild, M.F. :
Evidence of selection signatures that shape the Persian cat breed. Mamm Genome 27:144-55, 2016. Pubmed reference: 26956354 . DOI: 10.1007/s00335-016-9623-1.
Bertolini, F., Gandolfi, B., Kim, E.S., Haase, B., Lyons, L.A., Rothschild, M.F. :
Erratum to: Evidence of selection signatures that shape the Persian cat breed. Mamm Genome 27:156-157, 2016. Pubmed reference: 27007993 . DOI: 10.1007/s00335-016-9626-y.
Lyons, L.A., Erdman, C.A., Grahn, R.A., Hamilton, M.J., Carter, M.J., Helps, C.R., Alhaddad, H., Gandolfi, B. :
Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats. Dev Biol 409:451-8, 2016. Pubmed reference: 26610632 . DOI: 10.1016/j.ydbio.2015.11.015.
2010 Oechtering, G.U., Schlüter, C., Lippert, J.P. :
[Brachycephaly in dog and cat: a "human induced" obstruction of the upper airways]. Pneumologie 64:450-2, 2010. Pubmed reference: 20632241 . DOI: 10.1055/s-0030-1255513.
2003 Breit, S., Künzel, W., Oppel, M. :
The course of the nasolacrimal duct in brachycephalic cats. Anat Histol Embryol 32:224-7, 2003. Pubmed reference: 12919073 .
1986 Noden, D.M., Evans, H.E. :
Inherited homeotic midfacial malformations in Burmese cats. J Craniofac Genet Dev Biol Suppl 2:249-66, 1986. Pubmed reference: 2878018 .
Sponenberg, D.P., Graf-Webster, E. :
Hereditary meningoencephalocele in Burmese cats. J Hered 77:60, 1986. Pubmed reference: 2937834 .

Edit History

  • Created by Frank Nicholas on 02 Apr 2016
  • Changed by Frank Nicholas on 02 Apr 2016
  • Changed by Frank Nicholas on 19 May 2016
  • Changed by Frank Nicholas on 11 Jun 2020
  • Changed by Imke Tammen2 on 02 Feb 2023