OMIA 000197-9031 : Cleft palate in Gallus gallus

In other species: domestic cat , cattle , dog , horse , pig , rabbit , American mink , sheep

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 106250 (trait) , 106260 (trait) , 114300 (trait) , 119300 (trait) , 119500 (trait) , 119530 (trait) , 119540 (trait) , 119550 (trait) , 119570 (trait) , 119580 (trait) , 120433 (trait) , 129400 (trait) , 129810 (trait) , 129830 (trait) , 129900 (trait) , 164220 (trait) , 179400 (trait) , 181180 (trait) , 201180 (trait) , 216100 (trait) , 216300 (trait) , 218090 (trait) , 225000 (trait) , 231060 (trait) , 241850 (trait) , 242840 (trait) , 244300 (trait) , 255995 (trait) , 258320 (trait) , 260150 (trait) , 261800 (trait) , 268300 (trait) , 277170 (trait) , 301815 (trait) , 303400 (trait) , 600331 (trait) , 600460 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal Recessive Lethal

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2020

Cross-species summary: Congenital fissure (split) that involves the hard or soft palate (roof of the mouth). Also known as palatoschisis.

Species-specific name: Cleft primary palate

Species-specific symbol: cpp

History: Youngworth and Delany (2020): "The [cpp] mutation was first described under the name ectrodactyly (ec) and arose in a line carrying another autosomal recessive mutation named scaleless (sc). The homozygous sc mutation, as its name implies, results in absence of scales, as well as foot pads, spurs and most feather follicles, but otherwise does not cause craniofacial or limb defects. (Abbott & MacCabe 1966). The double sc/ec mutants were observed with these sc defects as well as an absent upper palate and abnormal hindlimbs (Abbott & MacCabe 1966). Outcrosses of the sc/ec carriers to normally feathered birds produced carriers who were test mated and then crossed to produce mutants with the palate abnormality alone to show that the mutations were unlinked (notably, the hindlimb abnormality occurred only in the double sc/ec mutants). The ec mutation was later backcrossed for nine generations into a highly inbred Single Comb White Leghorn line (UCD 003) and renamed cleft primary palate to reflect the key phenotype of the single mutation. The line was then closed to create the separate congenic inbred line UCD cpp.003, estimated to have greater than 99% DNA identity to UCD 003 outside of the introgressed mutation-encoding region given the number of backcrosses of the cpp-containing line to the highly inbred UCD 003 background line (Abplanalp 1992). Birds of the UCD cpp.003 line are test mated to verify carrier status prior to annual reproduction."

Inheritance: As summarised by Youngworth and Delany (2020), "The fact that carriers are phenotypically normal with consistent Mendelian ratios of mutants to carriers and non-carriers shows that the mutation is probably a recessive single-gene defect (Abbott & MacCabe 1966)."

Mapping: Youngworth and Delany (2020): "the candidate region for the cpp developmental mutation was established as a ca. 5.1 Mb region of chicken chromosome 11 (GGA 11) through the use of a 600K Affymetrix SNP array". Subsequent fine-mapping reduced this region to 4.9Mb.

Molecular basis: Youngworth and Delany (2020) reported that the "candidate region (4.9 Mb) was sequenced via capture array in a cohort of 24 individuals, including carriers, mutants and their wild type (wt) siblings", ultimately revealing "a frameshift mutation in ESRP2" as a likely causal variant, namely a "single-base deletion (galGal5 chr11:3 384 959; ss5200091912) [which] is predicted to cause a frameshift mutation in ESRP2 affecting multiple transcripts".

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
ESRP2 epithelial splicing regulatory protein 2 Gallus gallus 11 NC_052542.1 (2888839..2942778) ESRP2 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.

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
Cleft primary palate ESRP2 deletion, small (<=20) Naturally occurring variant GRCg6a 11 g.3284041del ss5200091912 2020 32162363


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.
2020 Youngworth, I.A., Delany, M.E. :
Mapping of the chicken cleft primary palate mutation on chromosome 11 and sequencing of the 4.9 Mb linked region. Anim Genet :, 2020. Pubmed reference: 32162363. DOI: 10.1111/age.12927.
2004 MacDonald, ME., Abbott, UK., Richman, JM. :
Upper beak truncation in chicken embryos with the cleft primary palate mutation is due to an epithelial defect in the frontonasal mass. Dev Dyn 230:335-49, 2004. Pubmed reference: 15162512. DOI: 10.1002/dvdy.20041.
1975 Juriloff, D.M., Roberts, C.W. :
Genetics of cleft palate in chickens and the relationship between the occurrence of the trait and maternal riboflavin deficiency. Poult Sci 54:334-46, 1975. Pubmed reference: 1178592.
1974 Roberts, C.W., Jain, G., Juriloff, D.M., Gehring, J. :
Selection of a cleft palate line of chickens beginning with the relationship between the trait and the level of riboflavin in the diet. Poult Sci 53:700-13, 1974. Pubmed reference: 4833306.
1966 Abbott, U.K., MacCabe, J.A. :
Ectrodactyly: a new embryonic lethal mutation in the chicken. J Hered 57:207-11, 1966. Pubmed reference: 5971042.

Edit History

  • Created by Frank Nicholas on 06 Sep 2005
  • Changed by Frank Nicholas on 14 Mar 2020
  • Changed by Frank Nicholas on 15 Mar 2020