OMIA:000317-9913 : Ears, crop in Bos taurus (taurine cattle)

Categories: Hearing / vestibular / ear phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 612109 (trait) , 142992 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal dominant with variable expressivity

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2013

Species-specific name: Notched ears; Nicked ears

Species-specific symbol: CE

Species-specific description: Koch et al. (2013) suggested the following nomenclature: CE-0 for homozygous wild type; CE-1 for heterozygotes; and CE-2 for homozygous duplication.

History: This disorder was first documented by Yamane (1915).

Inheritance: In the original report, Yamane (1915) provided pedigree evidence that implied Mendelian inheritance. Later reports (Wriedt, 1925; MacDonald, 1957; Scheider et al., 1994) were consistent with autosomal dominance with variable expressivity (suggestive of a multifactorial underlying trait, with one gene of large effect). Koch et al. (2013) reached the same conclusion from a pedigree analysis, and were able to trace all cases back to a single bull born in 1943.

Mapping: From a GWAS on 32 affected and 36 control Highland cattle, each genotyped with the Illumina bovine HD SNP chip (yielding 519,828 informative SNPs), Koch et al. (2013) mapped this trait to a 4Mb region of chromosome BTA6 (106Mb to 110Mb; UMD3 assembly).

Molecular basis: Among the 64 genes in the mapped region (see Mapping section), Koch et al. (2013) reported that HMX1 (which encodes a transcription factor) stood out as a "striking functional [comparative] candidate" (based on known mutations in humans, mice and rats). Whole-genome sequencing of a severely affected cow (assumed to be homozygous) revealed "6 non-synonymous DNA variants within the two coding exons of HMX1 and two structural variants within the downstream highly conserved region". Genotyping by sequencing in other animals excluded all but one of the structural variants, namely a 76bp duplication (Copy Number Variant; CNV), which was confirmed as the causal mutation by subsequent genotyping in 40 affecteds and 80 control Highland cattle, as well as in 144 cattle from a range of other breeds. As reported by Koch et al. (2013), "The affected ultra-conserved enhancer is located 148 kb apart of the coding region of HMX1 . . . . The sequence of the 76 bp duplication is highly conserved . . . . In silico prediction revealed several transcription factor binding sites indicating the potential functional relevance of this region".

Clinical features: As reported by Koch et al. (2013): "Crop ears in Highland cattle generally affect both ears more or less symmetrically, with a nick on the tip of the ear . . . . Crop ears are already present at birth and occur both in male and female cattle. We classified the crop ear phenotype into 2 general categories of varying severity: in category 1 the notches are mild to moderate and the ear cartilage appears normal or is only mildly deformed . . . . Category 2 is defined by clearly shortened ears, large notches and prominent (and slightly caudally twisted) upper edges of the ear cartilage above the notches . . . . However, the phenotypic severity of crop ears varies greatly within both categories."

Breeds: Ayrshire (Cattle) (VBO_0000120), Highland (Cattle) (VBO_0000234), Jersey (Cattle) (VBO_0000250).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
HMX1 H6 family homeobox 1 Bos taurus 6 NC_037333.1 (115036434..115031393) HMX1 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 Year Published PubMed ID(s) Acknowledgements
727 Highland (Cattle) Ears, crop HMX1 insertion, gross (>20) Naturally occurring variant 6 76bp duplication of 106,720058 to 106,720,133 on BTA6; UMD3 reference assembly 2013 24194898

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:000317-9913: 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.

2013 Koch, C.T., Bruggmann, R., Tetens, J., Drögemüller, C. :
A non-coding genomic duplication at the HMX1 locus is associated with crop ears in Highland cattle. PLoS One 8:e77841, 2013. Pubmed reference: 24194898. DOI: 10.1371/journal.pone.0077841.
1994 Scheider, A., Schmidt, P., Distl, O. :
[Inheritance of Crop Ears in Highland Cattle] Berliner und Munchener Tierarztliche Wochenschrift 107:348-352, 1994. Pubmed reference: 7802624.
1957 MacDonald, M.A. :
Notched ears in New Zealand dairy cattle Journal of Heredity 48:244-247, 1957.
1925 Wriedt, C. :
Vererbliche Scharten an den Ohren des Rindes. Z Tierzucht Zuchtungsbiol 3:235–238, 1925.
1922 Lush, J.L. :
An hereditary notch in the ears of Jersey cattle Journal of Heredity 13:8-13, 1922. DOI: 10.1093/oxfordjournals.jhered.a102155.
1915 Yamane, J. :
On the inheritance of an aural abnormality in the Ayrshire Cattle. Journal of the College of Agriculture, Tohoku Imperial University, Sapporo, Japan 6(7):166-170, 1915.

Edit History

  • Created by Frank Nicholas on 18 Oct 2010
  • Changed by Frank Nicholas on 08 Nov 2013
  • Changed by Imke Tammen2 on 08 Oct 2023