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Table 2 Loss-of-function variants detected in case and control cohorts

From: Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs

Symbol CDS changea Protein change dbSNP identifier Cases Control participants Consequence EVS European MAF ExAC non-Finnish European MAF
ADAM29 c.2020A > T p.Lys674Ter 1 0 Stop-gained 0 0
CASP8 c.379C > T p.Arg127Ter 1 0 Stop-gained 0 0
CDKN2A c.225_243delCGCCACTCTCACCCGACCC p.Ala76CysfsTer64 1 0 Frame shift 0 0
CDKN2B c.149_150delCG p.Ala50AspfsTer36 0 1 Frame shift 0 < 0.0001
DCLRE1B c.189 + 1G > C   1 0 Splice donor 0 0
DCLRE1B c.256G > T p.Gly86Ter 0 1 Stop-gained 0 0
FTO c.11delC p.Pro5ArgfsTer13 1 0 Frame shift 0 0
LGR6 c.858-2A > C   1 0 Splice acceptor < 0.0001 < 0.0001
MUS81 c.1314delC p.Pro439LeufsTer6 1 0 Frame shift 0 0
MUS81 c.1062delC p.Arg355GlyfsTer2 0 1 Frame shift 0 0
NFRKB c.2149G > T p.Glu717Ter 1 0 Stop-gained 0 0
NFRKB c.794C > G p.Ser265Ter 0 1 Stop-gained 0 < 0.0001
NRIP1 c.40_41insT p.Asp14ValfsTer25 1 0 Frame shift 0 0
NRIP1 c.2750C > G p.Ser917Ter 1 0 Stop-gained 0 0
NRIP1 c.1968dupT p.Gly657TrpfsTer5 1 0 Frame shift 0 0
PDE4D c.2400_2410dupTGTCATAGATG p.Asp804ValfsTer3 1 0 Frame shift 0 0
RAD51B c.139C > T p.Arg47Ter rs200355697 2 0 Stop-gained 0 0.0001
SETMAR c.823_826delAAAG p.Glu276GlyfsTer2 1 0 Frame shift 0 < 0.0001
SETMAR c.706C > T p.Arg236Ter 0 1 Stop-gained 0 0.0001
SETMAR c.1635C > G p.Tyr545Ter 0 1 Stop-gained 0 0
SLC4A7 c.1663G > T p.Gly555Ter 1 0 Stop-gained 0 0
SNX32 c.1111C > T p.Arg371Ter 1 0 Stop-gained 0 < 0.0001
SNX32 c.825 + 2 T > G   1 0 Splice donor 0 0
TCF7L2 c.1804_1805insAAT p.Glu602_Glu603insTer 0 1 Stop-gained 0 0
TET2 c.1085_1086insT p.Pro363SerfsTer6 1 0 Frame shift 0 0
TET2 c.2072delC p.Thr691MetfsTer9 1 0 Frame shift 0 0
TET2 c.3646C > T p.Arg1216Ter 1 0 Stop-gained 0 0
TET2 c.4361_4362insG p.Arg1455GlnfsTer23 1 0 Frame shift 0 0
TET2 c.3812_3820delGCGCCTGTC p.Cys1271_Gln1274delinsTer 1 0 Stop-gained 0 0
TET2 c.832C > T p.Gln278Ter 0 1 Stop-gained 0 0
TET2 c.1458delC p.Asn486LysfsTer11 0 1 Frame shift 0 0
TPK1 c.185 + 1G > A   0 1 Splice donor 0 0
USHBP1 c.1220 + 1G > T   rs144791770 1 0 Splice donor 0.0002 0.0001
USHBP1 c.258dupA p.Val87SerfsTer103 0 1 Frame shift 0.0001 < 0.0001
ZNF226 c.1229_1230delAA p.Arg411SerfsTer11 1 0 Frame shift 0 0.0001
ZNF226 c.2239C > T p.Arg747Ter 1 0 Stop-gained 0 0
ZNF226 c.2380G > T p.Glu794Ter rs201830106 0 1 Stop-gained 0.0007 0.0003
ZNF226 c.582delT p.Asn194LysfsTer41 0 1 Frame shift 0 0
  1. Abbreviations: CDS Coding DNA sequence, EVS Exome Variant Server, ExAC Exome Aggregation Consortium, MAF Minor allele frequency, dbSNP Single-nucleotide polymorphism database
  2. aCanonical transcript for each gene according to Ensembl definition