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Table 1 Genotypes of four variants compatible with recessive inheritance

From: A nonsense mutation in PLD4 is associated with a zinc deficiency-like syndrome in Fleckvieh cattle

Chr Position NCBI reference ID Variant Genotypes Gene Effect
Calf 58952 41 animals
21 70,679,787 rs381259516 InDel del/del del/G G/G intergenic -
21 70,842,696 rs384306864 SNP TT CC CC INF2 p.H1231Y
21 71,001,232 rs378824791 SNP AA GG GG PLD4 p.W215X
21 71,315,111 rs385301007 SNP TT CC CC LOC100299595 (=PACS2) intron 30
  1. Whole-genome re-sequencing of 43 animals revealed 7,660 polymorphic sites within the 1,032 kb segment on BTA 21. Among them, three SNPs and one InDel agree with the supposed inheritance pattern (i.e., the affected calf is homozygous for the alternative allele and the controls are heterozygous or homozygous for the reference allele). 58952 is a healthy animal being homozygous for the disease-associated haplotype.