Missense single nucleotide variants affecting CYP3A catalytic activity are present in Limousine cattle

Figures & data

Table 1. Cattle cytochrome P450 3A missense single-nucleotide variants subject of investigation in the present study: IDs, functional impact on CYP3A activity and frequency in Limousine cattle breed.

Ref. ID	DNA variant*	Amino acid variant	Impact on CYP3A activity	Genotype frequency (%, n)	Minor allele’s frequency	Chi-square test p value**
rs384467435	NM_001099367.1:c.589G > A	NP_001092837.1:p.Gly197Ser	–50% TST 6β-hydroxylation	WT/WT: 72.1% (155/215)
				WT/MUT: 24.2% (52/215)	0.16	0.179
				MUT/MUT: 3.7% (8/215)
rs433125080	NM_001099367.1:c.866C > T	NP_001092837.1: p.Ala289Val	–50% TST 6β-hydroxylation	WT/WT: 100% (215/215)	–	Not applicable
rs454167819	NM_001099367.1:c.1162A > G	NP_001092837.1:p.Ile388Val	–50% TST 6β-hydroxylation	WT/WT: 94.4% (204/215)
				WT/MUT: 5.1% (11/215)	0.03	Not applicable
				MUT/MUT: 0% (0/215)
NA	NM_001075888.2:c.1122G > T	NP_001069356.1:p.Glu374Asp	+258% TST 16β-hydroxylation	WT/WT: 100% (215/215)	–	Not applicable
rs137124349	NM_174513.3:c.1051G > A	NP_776956.2:p.Val351Ile	+317% NIF oxydation	ND	–	Not applicable

Ala: alanine; Asp: aspartic acid; CYP3A: cytochrome P450 3A; Glu: glutamic acid; Gly: glycine; Ile: isoleucine; MUT/MUT: mutant genotype; NA: not available; ND: not detectable; NIF: nifedipine; Ref. ID: reference identification tag; Ser: serine; TST: testosterone; Val: valine; WT/MUT: heterozygous genotype; WT/WT: wild type genotype.

*Variant nomenclature is consistent with the previous paper of Giantin et al. (2019), in which UMD3.1 assembly was used as reference genome. **Hardy-Weinberg Equilibrium (HWE) was assessed by means of Chi-square test. A value of p > .05 was obtained for rs384467435, denoting a consistency with HWE.

Figure 1. Output of NM_001099367.1:c.589G > A (A) and NM_001099367.1:c.1162A > G (B) melting curve genotyping assays (LightCycler 480 software release 1.5, Roche). WT/WT (wild type), WT/MUT (heterozygous), and MUT/MUT (mutant) genotypes are indicated with green, red and blue curves, respectively. The BLANK (no template control) is shown in purple.

Giantin M, Rahnasto-Rilla M, Tolosi R, Lucatello L, Pauletto M, Guerra G, Pezzato F, Lopparelli RM, Merlanti R, Carnier P, et al. 2019. Functional impact of cytochrome P450 3A (CYP3A) missense variants in cattle. Sci Rep. 9(1):19672.

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