OMIA:002178-9823 : Abortion, BBS9 and BMPER-related in Sus scrofa (pig)

Categories: Mortality / aging (incl. embryonic lethal)

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 615986 (trait) , 608022 (trait) , 608699 (gene) , 607968 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive lethal

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2018

Species-specific name: SSC18 haplotype

Species-specific description: Derks et al. (2018) describe "a lethal 212kb deletion with pleiotropic effects on two different genes, one resulting in fetal death in homozygous state (BMPER), and the other increasing growth (BBS9) in heterozygous state. We provide strong evidence for balancing selection resulting in an unexpected high frequency of a lethal allele in the population."

Mapping: Derks et al. (2018) analysed a population of 23,722 purebred Large White pigs to identify lethal alleles. "The animals were genotyped on the Illumina GeneSeek custom 50K SNPchip." To identify the missing homozygote haplotypes, "the SS18 haplotype [was tested] for the expected number of homozygotes using both parents haplotype information." (Edited by Emmi Payten 24/8/2021)

Molecular basis: Derks et al. (2018) identified "a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. ... The mutant transcript results in a frameshift introducing 11 novel amino acids before a premature stop codon, generating a truncated BBS9 protein ...[and reduces] expression of the downstream BMPER gene, an essential gene for normal foetal development." (Edited by Emmi Payten 24/8/2021)

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

Clinical features: Derks et al. (2018): "Homozygous del/del animals die mid- to late-gestation, as observed from high increase in numbers of mummified piglets resulting from carrier-by-carrier crosses. ...heterozygous carriers exhibit increased growth rate, an important selection trait in pig breeding. Increased growth and appetite together with a lower birth weight for carriers of the BBS9 null allele in pigs is analogous to the phenotype described in human and mouse for (naturally occurring) BBS9 null-mutants."

Prevalence: Derks et al. (2018) estimated a 10.8% carrier frequency (5.4% allele frequency) in the Large White population studied. There were no homozygous individuals identified in the population. The authors traced the origin of the deletion in the population over a 12 year period (2006-2018). The carrier frequency was high (>15%) from 2006-2010 and then stabilised from 2012 onwards (~10%). (Edited by Emmi Payten 24/8/2021)

Breed: Large White (Pig) (VBO_0001163).
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 genes:

Symbol Description Species Chr Location OMIA gene details page Other Links
BMPER BMP binding endothelial regulator Sus scrofa 18 NC_010460.4 (39664010..39417830) BMPER Homologene, Ensembl , NCBI gene
BBS9 Bardet-Biedl syndrome 9 Sus scrofa 18 NC_010460.3 (44336434..44115079) BBS9 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
1049 Large White (Pig) Abortion, BBS9 and BMPER-related BBS9 deletion, gross (>20) Naturally occurring variant Sscrofa11.1 18 g.39817373_40029300del Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene" 2018 30231021

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:002178-9823: 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.

2021 Derks, M.F.L., Steensma, M. :
Review: Balancing selection for deleterious alleles in livestock. Front Genet 12:761728, 2021. Pubmed reference: 34925454. DOI: 10.3389/fgene.2021.761728.
2018 Derks, M.F.L., Lopes, M.S., Bosse, M., Madsen, O., Dibbits, B., Harlizius, B., Groenen, M.A.M., Megens, H.J. :
Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome. PLoS Genet 14:e1007661, 2018. Pubmed reference: 30231021. DOI: 10.1371/journal.pgen.1007661.
2017 Derks, M.F.L., Megens, H.J., Bosse, M., Lopes, M.S., Harlizius, B., Groenen, M.A.M. :
A systematic survey to identify lethal recessive variation in highly managed pig populations. BMC Genomics 18:858, 2017. Pubmed reference: 29121877. DOI: 10.1186/s12864-017-4278-1.

Edit History

  • Created by Frank Nicholas on 21 Mar 2019
  • Changed by Imke Tammen2 on 18 Apr 2021
  • Changed by Imke Tammen2 on 27 May 2021
  • Changed by Imke Tammen2 on 24 Aug 2021