OMIA:002594-9823 : N-acetyl-galactosamine, reduced intestinal concentration in Sus scrofa (pig)

Categories: Digestive / alimentary phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 110300 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal incomplete dominant

Considered a defect: unknown

Key variant known: yes

Year key variant first reported: 2022

Species-specific name: intestinal microbiota/microbiome composition

Species-specific description: Yang et al. (2022): "we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine."

Molecular basis: Yang et al. (2022): "A 2.3 kb deletion [in the ABO gene] encompassing the last exon has been reported in pigs [Choi et al., 2018]. We showed that it was in near-perfect LD (r2 ≥ 0.94) with the lead SNPs in our population ... . We confirmed its boundaries and showed that it results from an intrachromosomal recombination between short interspersed nuclear elements (SINEs). ... Our results indicate that the 2.3 kb deletion creates a null allele ... and that is a very strong candidate for the causative miQTL mutation ... ."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
ABO Sus scrofa 1 NC_010443.5 (272935316..272912239) ABO 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 Year Published PubMed ID(s) Acknowledgements
1504 N-acetyl-galactosamine intestinal concentration ABO deletion, gross (>20) Naturally occurring variant 1 2.3kb deletion encompassing exon 8 2022 35477154

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:002594-9823: 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.

2023 Huang, L., Chen, C. :
Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives. Gut Microbes 15:2205410, 2023. Pubmed reference: 37122143. DOI: 10.1080/19490976.2023.2205410.
2022 Yang, H., Wu, J., Huang, X., Zhou, Y., Zhang, Y., Liu, M., Liu, Q., Ke, S., He, M., Fu, H., Fang, S., Xiong, X., Jiang, H., Chen, Z., Wu, Z., Gong, H., Tong, X., Huang, Y., Ma, J., Gao, J., Charlier, C., Coppieters, W., Shagam, L., Zhang, Z., Ai, H., Yang, B., Georges, M., Chen, C., Huang, L. :
ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 606:358-367, 2022. Pubmed reference: 35477154. DOI: 10.1038/s41586-022-04769-z.
2018 Choi, M.K., Le, M.T., Cho, H., Yum, J., Kang, M., Song, H., Kim, J.H., Chung, H.J., Hong, K., Park, C. :
Determination of complete sequence information of the human ABO blood group orthologous gene in pigs and breed difference in blood type frequencies. Gene 640:1-5, 2018. Pubmed reference: 28966132. DOI: 10.1016/j.gene.2017.09.047.

Edit History

  • Created by Imke Tammen2 on 15 Nov 2022
  • Changed by Imke Tammen2 on 15 Nov 2022