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Table 2 Missense and nonsense variants that were significantly (p < 5*10−9) associated with fertility traits

From: Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences

Trait

BTA

Position

p-value

Gene

Variant

PolyPHEN2

SIFT

NRH

17

70,724,328

1.63 × 10−16

GAS2L1

p.P655L

unknown

deleterious (low confidence)

IFLH

2.20 × 10−11

NRH

17

71,084,044

8.03 × 10−17

ASCC2

p.P42L

probably damaging

deleterious

IFLH

3.52 × 10−11

NRH

17

72,747,746

8.78 × 10−10

SLC5A4

p.G608Sa/p.G235Sb

probably damaging

deleterious

NRH

17

72,815,579

1.61 × 10−9

ENSBTAG00000048030

p.Y108*

NRH

17

73,344,409

1.39 × 10−9

CABIN1

p.R651Q

benign

tolerated

NRH

17

73,393,194

1.09 × 10−9

CABIN1

p.A1721V

benign

tolerated (low confidence)

NRH

17

73,442,633

2.37 × 10−9

ENSBTAG00000046900

p.T234A

benign

tolerated

NRC

17

74,739,013

3.25 × 10−9

CDC45L

p.A263T

benign

tolerated

NRH

3.49 × 10−9

  1. Trait: NRC non-return rate in heifers, NRH non-return rate in heifers, IFLH interval from first to last insemination in heifers
  2. BTA: Chromosome
  3. P-value: From GWAS with EMMAX
  4. Variant: Amino acid change caused by the variant
  5. PolyPhen2: Predicted effect of the variant on the protein function from PolyPhen2
  6. SIFT: Predicted effect of the variant on the protein function from SIFT obtained via Variant effect predictor (VEP)
  7. a/bThe transcripts ENSBTAT00000010678a and ENSBTAT00000052915b for SLC5A4