Table 4 Candidate variants potentially explaining the identified haplotype regions.

From: Four novel candidate causal variants for deficient homozygous haplotypes in Holstein cattle

Haplotype

Gene

OMIM

Variant description

Genomic positiona

Description

Transcriptb

Coding DNA change

Protein change

HH21c

NOTCH3

600276

chr7:7913459

3 bp deletion (inframe deletion)

XM_003586246.3

c.129_131delTTG

p.Cys44del

HH3d

SMC2e

605576

chr8:93753358

SNV (missense)

XM_015472668.2

c.3404T > C

p.Phe1135Ser

HH25

RIOX1

611919

chr10:84938370

30 bp deletion (inframe deletion)

NM_001099702.1

c.396_425delGGCGCAGACCCCGGCGGCACGCTTGGTGGA

p.Ala133_Glu142del

HH13f

KIR2DS1

604952

chr18:62758881

SNV (nonsense)

NM_001097567.1

c.475C > T

p.Gln159*

HH35

PCDH15

605514

chr26:5325675

SNV (missense)

XM_015460562.2

c.2599C > G

p.Leu867Val

  1. aAccording to the reference sequence ARS-UCD1.231.
  2. bAccording to NCBI Annotation Release 10691.
  3. cHaplotype described before as 175.5 and 07-126 by VanRaden et al. and Sahana et al., respectively13,18.
  4. dHaplotype previously described by VanRaden et al., McClure et al., Sahana et al. and Wu et al.13,18,19,87.
  5. eVariant previously detected by McClure et al.24.
  6. fHaplotype previously described by Fritz et al.16.
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