Skip to main content
. 2022 Mar 31;12:5435. doi: 10.1038/s41598-022-09403-6

Table 1.

Previously identified lethal haplotype regions and their associated candidate causal variants in Holstein cattle.

Haplotype name Associated disorder Gene OMIA Variant description Publications
chr Positiona Description Transcript of interestb Coding DNA change Protein change
HH0 Brachyspina FANCI 000151-9913 21 21,184,869–21,188,198 Gross deletion (frameshift) 3.3 kb deletion 19,20,27,85,86
HH1 Embryonic lethality APAF1 000001-9913 5 62,810,245 SNV (nonsense) NM_001191507.1 c.1702C > T p.Gln568* 13,16,22,85
HH2 Embryonic lethality IFT80 001823-9913 1 107,172,616 SNV (frameshift) XM_024984168.1 c.747delT p.Leu250fs 13,24,28,85
HH3 Abortion SMC2 001,824-9913 8 93,753,358 SNV (missense) XM_015472668.2 c.3404T > C p.Phe1135Ser 13,18,19,85,87
HH4 Abortion GART 001826–9913 1 1,997,582 SNV (missense) NM_001040473.2 c.869A > C p.Asn290Thr 16,27,85
HH5 Abortion TFB1M 001941-9913 9 93,223,651–93,370,998 Gross deletion 139 kb deletion 26,27,85
HH6 Embryonic lethality SDE2 002149-9913 16 29,020,700 SNV (start-lost) NM_001099065.2 c.2T > C p.Met1? 27
HH7 Embryonic lethality CENPU 001830-9913 27 15,123,636 5 bp deletion (splice site) XM_002698654.5 c.15123637_15123640delTTACT 17
HHB Bovine leukocyte adhesion deficiency (BLAD) ITGB2 000595-9913 1 144,770,078 SNV (missense) NM_175781.1 c.383A > G p.Asp128Gly 51,85
HHC Complex vertebral malformation (CVM) SLC35A3 001340-9913 3 43,261,945 SNV (missense) NM_001105386.1 c.538G > T p.Val180Phe 21,85,88
HHD Deficiency of uridine monophosphate synthase (DUMPS) UMPS 000262-9913 1 69,151,931 SNV (nonsense) NM_177508.1 c.1213C > T p.Arg405* 85,89,90
CDH Cholesterol deficiency; juvenile mortality APOB 001965-9913 11 77,891,733 Large insertion (frameshift) ERV insertion 26,29,30,53,85

aAccording to the reference sequence ARS-UCD1.231.

bAccording to the NCBI Annotation Release 10691.