OMIA:002178-9823 : Abortion, BBS9 and BMPER-related in Sus scrofa
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)
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).
|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|
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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|
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.|
- 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