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Table 3 Functionally important variants located within LCORL gene haplotype on chromosome 6 segregating in Nordic Red cattle; RDCDNK, RDCSWE, and RDCFIN are Nordic Red cattle from Denmark, Sweden, and Finland, respectively

From: Loci associated with adult stature also affect calf birth survival in cattle

Position (bp)

Annotation

Allele frequency in RDCDNK

Allele frequency in RDCSWE + RDCFIN

38776669

Missense variant; SIFT1: tolerated(1); GERP2 = −5.05

0 = 0.967; 1 = 0.033

0 = 0.868; 1 = 0.132

38777311

Missense variant; SIFT: deleterious(0.02); GERP = 3.13

0 = 0.633; 1 = 0.367

0 = 0.971; 1 = 0.029

38779781

Missense variant; SIFT: deleterious(0.02); GERP = 4.31

0 = 1.000

0 = 0.941; 1 = 0.059

38808241

Missense variant; SIFT: deleterious(0.04); GERP = 0.886

0 = 0.522; 1 = 0.478

0 = 0.971; 1 = 0.029

38844538

Missense variant; SIFT: tolerated(1); GERP = 2.51

0 = 0.000; 1 = 1.000

0 = 0.985; 1 = 0.015

38844605

Frameshift variant & splice region variant & feature truncation

0 = 0.000; 1 = 1.000

0 = 0.000; 1 = 1.000

38846294

Splice donor variant; GERP = 4.4

0 = 0.943; 1 = 0.057

0 = 0.926; 1 = 0.074

38991938

Inframe insertion

0 = 1.000

0 = 0.865; 1 = 0.135

  1. 1SIFT = Sorting Intolerant From Tolerant predicted score [56]; 2GERP = Genomic Evolutionary Rate Profiling predicted score [57].