Table 3.
Allele frequency of missense variants.
| Variant of casein gene | BTA positiona | Allele | Amino acid | Protein seq. positionb | SNP ID | Variant frequency | ||
|---|---|---|---|---|---|---|---|---|
| DSN | HF | All breeds | ||||||
| CSN1S1*B | 6:87157262 | A/G | Glu/Gly | 207 (192) | rs43703010 | 1.0 | 0.995 | 0.944 |
| CSN2*A 1 | 6:87181619 | T/G | His/Pro | 82 (67) | rs43703011 | 0.827 | 0.340 | 0.295 |
| CSN2*A 2 | 6:87181619 | T/G | His/Pro | 82 (67) | rs43703011 | 0.156 | 0.562 | 0.592 |
| CSN2*I | 6:87181542 | T/G | Met/Leu | 108 (93) | rs109299401 | 0.017 | 0.059 | 0.036 |
| CSN1S2*A | 6:87266177 | C/T | Ser/Phe | 23 (8) | rs441966828 | 1.0 | 1.0 | 0.994 |
| CSN3*A | 6:87390576 | T/C | Ile/Thr | 157 (136) | rs43703015 | |||
| 6:87390612 | C/A | Ala/Asp | 169 (148) | rs43703016 | 0.833 | 0.752 | 0.628 | |
| 6:87390632 | A/G | Ser/Gly | 176 (155) | rs43703017 | ||||
| CSN3*B | 6:87390576 | T/C | Ile/Thr | 157 (136) | rs43703015 | 0.133 | 0.203 | 0.341 |
| 6:87390612 | C/A | Ala/Asp | 169 (148) | rs43703016 | ||||
| CSN3*E | 6:87390632 | A/G | Ser/Gly | 176 (155) | rs43703017 | 0.034 | 0.045 | 0.030 |
Allele frequencies of missense variants in CSN1S1, CSN2, CSN1S2, and CSN3 in DSN compared to Holstein Friesian (HF) and other breeds. For each variant, we list the alleles as ref/alt. In a bold font we highlight the SNP allele and resulting amino acid which causes the casein variant. As an example, the CSN2*A1 and CSN2*A2 variants are caused by a SNP on the same position 6:87181619. In the case of A1, the T-allele causes a histidine to be incorporated into the protein sequence. The A2 variant is defined as a G on the same position, leading to a proline in the resulting protein.
Bos taurus autosome (BTA) CSN1S1*B (ENSBTAG00000007695), CSN2*A2 (ENSBTAG00000002632), CSN1S2*A (ENSBTAG00000005005), and CSN3*A (ENSBTAG00000039787).
Positions of amino acids according to the reference protein sequence from Ensembl Release 93 UMD3.1 assembly. Positions in the mature protein are given in parentheses.