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
Disease-related: 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 |
Variants
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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]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70
References
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