Supplementary table 1A. Variants detected in breast cancer-affected members of family 1 Gene DESCRIPTION KEGG Pathway ID KEGG Pathway Description Chr Position RefSeq ExonChange Func ESP6500 1000 Genome dbSNP137 PolyPhen2 Distribution Frequency Nucleotide Amino acid Score Prediction 1 2 3 4 6 7 8 GPRIN1 G protein regulated inducer of neurite outgrowth 1 chr5 176026123 NM_052899 exon2 c.T713C p.L238S exonic 0.91 D -+++++- 5 ZNF335 zinc finger protein 335 chr20 44598182 NM_022095 exon3 c.T350C p.M117T exonic 1.00 D -+++--+ 4 LRRC66 leucine rich repeat containing 66 chr4 52861746 NM_001024611 exon4 c.A1442T p.D481V exonic 0.96 D --+++-+ 4 NBPF16 neuroblastoma breakpoint family, member 16 chr1 148756665 NM_001102663 exon16 c.G1994T p.G665V exonic 0.92 D ++-++-- 4 GPR116 G protein-coupled receptor 116 chr6 46826012 NM_001098518 exon17 c.G3628C p.E1210Q exonic 1.00 D -+++--- 3 ANKRD20A1 ankyrin repeat domain 20 family, member A1 chr9 67934829 NM_001012419 exon4 c.G599A p.R200Q splicing 1.00 D --++--+ 3 RBMXL1 RNA binding motif protein, X-linked-like 1 chr1 89449011 NM_019610 exon2 c.C499G p.P167A exonic 1.00 D +---++- 3 COL12A1 collagen, type XII, alpha 1 chr6 75864212 NM_004370 exon17 c.A3485C p.D1162A exonic 0.85 D --+--++ 3 ANKRD20A1 ankyrin repeat domain 20 family, member A1 chr9 67935957 NM_001012419 exon5 c.C682A p.Q228K exonic 0.81 P -+-++-- 3 ITGB1BP1 integrin beta 1 binding protein 1 chr2 9546989 NM_022334 exon6 c.T427A p.S143T exonic 0.75 P -+++--- 3 AVIL advillin chr12 58197038 NM_006576 exon15 c.T1954C p.W652R exonic 1.00 D ----++- 2 MYH3 myosin, heavy chain 3, skeletal muscle, embryonic hsa05416 Viral myocarditis chr17 10533244 NM_002470 exon39 c.A5573G p.D1858G exonic 1.00 D -+-+--- 2 RNF215 ring finger protein 215 chr22 30775768 NM_001017981 exon8 c.A1043G p.H348R exonic 1.00 D --++--- 2 ANKRD44 ankyrin repeat domain 44 chr2 197986226 NM_001195144 exon8 c.G736A p.A246T exonic 0.99 D ----++- 2 ITPR2 inositol 1,4,5-trisphosphate receptor, type 2 hsa05010 Alzheimer's disease chr12 26839489 NM_002223 exon11 c.C1073T p.P358L exonic 0.99 D ----+-+ 2 USP28 ubiquitin specific peptidase 28 chr11 113683049 NM_020886 exon16 c.A1921G p.S641G exonic 0.99 D --++--- 2 ZNF417 zinc finger protein 417 chr19 58421230 NM_152475 exon3 c.A416G p.Q139R exonic 0.99 D -++---- 2 ZNF587 zinc finger protein 587 chr19 58370196 NM_001204817 exon3 c.A413G p.Q138R exonic 0.99 D -++---- 2 TIGD2 tigger transposable element derived 2 chr4 90034310 NM_145715 exon1 c.C185T p.T62I exonic 0.99 D ----+-+ 2 NUP35 nucleoporin 35kDa chr2 184016246 NM_138285 exon5 c.G408C p.M136I exonic 0.98 D ----++- 2 FLG filaggrin chr1 152276761 NM_002016 exon3 c.A10601G p.N3534S exonic 0.98 D +---+-- 2 GOLGA8A golgin A8 family, member A chr15 34677275 NM_181077 exon7 c.G541A p.A181T exonic 0.96 D --+---+ 2 TEX15 testis expressed 15 chr8 30702074 NM_031271 exon1 c.C4460T p.T1487I exonic 0.88 D ----++- 2 ANKRD20A2 ankyrin repeat domain 20 family, member A2 chr9 42377496 NM_001012419 exon5 c.C682A p.Q228K exonic 0.81 P -+----+ 2 ACADVL acyl-CoA dehydrogenase, very long chain hsa01100 Metabolic pathways chr17 7125576 NM_001033859 exon8 c.A767T p.K256M exonic 0.81 P -+-+--- 2 GOLGA8A golgin A8 family, member A chr15 34674259 NM_181077 exon14 c.C1363T p.R455C exonic 0.70 P ---+--+ 2 C11orf82 chromosome 11 open reading frame 82 chr11 82643815 NM_145018 exon6 c.T1435A p.L479I exonic 0.63 P --++--- 2 ARID4B AT rich interactive domain 4B (RBP1-like) chr1 235346016 NM_031371 exon19 c.C1960T p.H654Y exonic 0.47 P -++---- 2 ANKRD20A1 ankyrin repeat domain 20 family, member A1 chr9 67938656 NM_001012419 exon6 c.C791G p.S264X stopgain 0.57 --+++-- 3 ABCC6 ATP-binding cassette, sub-family C (CFTR/MRP), memberhsa02010 6 ABC transporters chr16 16269844 NM_001171 exon21 c.2591-1G>T splicing - - + + - - - 2 ALDOA aldolase A, fructose-bisphosphate hsa01100 Metabolic pathways chr16 30066250 splicing - - - - + - + 2 PINK1 PTEN induced putative kinase 1 hsa05012 Parkinson's disease chr1 20972051 NM_032409 exon5 c.960-2A>G splicing - - + + - - - 2 ANAPC1 anaphase promoting complex subunit 1 hsa04914 Progesterone-mediated oocyte maturation chr2 112573216 NM_022662 exon28 c.C3328T p.R1110C exonic 1.00 D -----+- 1 CTBP2 C-terminal binding protein 2 hsa05220 Chronic myeloid leukemia chr10 126683225 NM_022802 exon5 c.G2213C p.R738P exonic 1.00 D ---+--- 1 ECI2 enoyl-CoA delta isomerase 2 hsa04146 Peroxisome chr6 4130638 NM_001166010 exon4 c.C379T p.R127W exonic 1.00 D ---+--- 1 GTF2I general transcription factor IIi hsa03022 Basal transcription factors chr7 74163734 NM_001518 exon24 c.C2243T p.P748L exonic 1.00 D --+---- 1 IGSF10 immunoglobulin superfamily, member 10 chr3 151156303 NM_001178145 exon2 c.T127G p.C43G exonic 1.00 D -+----- 1 KRT80 keratin 80 chr12 52579353 NM_001081492 exon2 c.C319T p.R107C exonic 1.00 D ---+--- 1 MAS1L MAS1 oncogene-like chr6 29454897 NM_052967 exon1 c.G783T p.R261S exonic 1.00 D ---+--- 1 PABPC3 poly(A) binding protein, cytoplasmic 3 chr13 25670625 NM_030979 exon1 c.G289C p.G97R exonic 1.00 D -----+- 1 TTLL7 tubulin tyrosine ligase-like family, member 7 chr1 84386943 NM_024686 exon11 c.G1277A p.R426Q exonic 1.00 D +------ 1 ZFAND4 zinc finger, AN1-type domain 4 chr10 46147441 NM_001128324 exon4 c.C301T p.R101C exonic 1.00 D -----+- 1 DHX35 DEAH (Asp-Glu-Ala-His) box polypeptide 35 chr20 37647477 NM_001190809 exon14 c.C1340T p.P447L exonic 1.00 D +------ 1 ERBB2IP erbb2 interacting protein hsa04621 NOD-like receptor signaling pathway chr5 65370916 NM_001253698 exon22 c.A3698G p.H1233R exonic 1.00 D -+----- 1 FRYL FRY-like chr4 48559492 NM_015030 exon34 c.A4103G p.N1368S exonic 1.00 D ---+--- 1 KRBA2 KRAB-A domain containing 2 chr17 8273461 NM_213597 exon2 c.G470A p.R157H exonic 1.00 D ---+--- 1 PABPC3 poly(A) binding protein, cytoplasmic 3 chr13 25671456 NM_030979 exon1 c.C1120T p.R374C exonic 1.00 D ------+ 1 PROSER1 proline and serine rich 1 chr13 39600439 NM_170719 exon5 c.C389T p.P130L exonic 1.00 D +------ 1 TES testis derived transcript (3 LIM domains) chr7 115892471 NM_015641 exon6 c.T1018C p.Y340H exonic 1.00 D ----+-- 1 WDR52 WD repeat domain 52 chr3 113115390 NM_001164496 exon14 c.G1754A p.R585H exonic 1.00 D ----+-- 1 CTBP2 C-terminal binding protein 2 hsa05220 Chronic myeloid leukemia chr10 126683235 NM_022802 exon5 c.G2203T p.V735F exonic 1.00 D ---+--- 1 FRG1 FSHD region gene 1 chr4 190883081 NM_004477 exon8 c.T734G p.L245R exonic 1.00 D ----+-- 1 OR4M1 olfactory receptor, family 4, subfamily M, member 1 hsa04740 Olfactory transduction chr14 20249380 NM_001005500 exon1 c.T899G p.M300R exonic 1.00 D ---+--- 1 LGALS9 lectin, galactoside-binding, soluble, 9 chr17 25965331 NM_002308 exon2 c.G82A p.G28R exonic 1.00 D --+---- 1 PIWIL4 piwi-like RNA-mediated gene silencing 4 hsa04320 Dorso-ventral axis formation chr11 94310519 NM_152431 exon4 c.A374G p.Q125R exonic 1.00 D +------ 1 SPESP1 sperm equatorial segment protein 1 chr15 69238630 NM_145658 exon2 c.G757T p.D253Y exonic 1.00 D +------ 1 TBC1D15 TBC1 domain family, member 15 chr12 72311484 NM_001146213 exon13 c.A1408C p.N470H exonic 1.00 D ---+--- 1 ITPR3 inositol 1,4,5-trisphosphate receptor, type 3 hsa05010 Alzheimer's disease chr6 33659653 NM_002224 exon54 c.G7406T p.G2469V exonic 1.00 D +------ 1 FRG1 FSHD region gene 1 chr4 190883080 NM_004477 exon8 c.C733A p.L245M exonic 0.99 D ----+-- 1 PCDH18 protocadherin 18 chr4 138452524 NM_019035 exon1 c.A719G p.N240S exonic 0.99 D -+----- 1 SLC30A7 solute carrier family 30 (zinc transporter), member 7 chr1 101387306 NM_001144884 exon8 c.G751C p.V251L exonic 0.99 D -+----- 1 UNC5A unc-5 homolog A (C. elegans) hsa04360 Axon guidance chr5 176306444 NM_133369 exon14 c.G2318A p.R773Q exonic 0.99 D +------ 1 EIF4G2 eukaryotic translation initiation factor 4 gamma, 2 hsa05416 Viral myocarditis chr11 10823596 NM_001042559 exon13 c.G1299T p.Q433H splicing 0.99 D +------ 1 MMRN1 multimerin 1 chr4 90857440 NM_007351 exon6 c.C2609T p.T870I exonic 0.99 D ----+-- 1 PEAK1 pseudopodium-enriched atypical kinase 1 chr15 77472182 NM_024776 exon5 c.A2087C p.E696A exonic 0.99 D -+----- 1 RGPD5 RANBP2-like and GRIP domain containing 5 chr2 111325017 NM_005054 exon4 c.C341A p.A114E exonic 0.99 D ---+--- 1 SGPL1 sphingosine-1-phosphate lyase 1 hsa01100 Metabolic pathways chr10 72628128 NM_003901 exon8 c.A642G p.I214M exonic 0.99 D -----+- 1 GPRIN1 G protein regulated inducer of neurite outgrowth 1 chr5 176026136 NM_052899 exon2 c.G700T p.D234Y exonic 0.99 D ----+-- 1 CTTN cortactin hsa05131 Shigellosis chr11 70279803 NM_001184740 exon16 c.G1384A p.A462T exonic 0.99 D ---+--- 1 CYYR1 cysteine/tyrosine-rich 1 chr21 27938648 NM_052954 exon2 c.A113T p.Y38F exonic 0.99 D +------ 1 ARSD arylsulfatase D chrX 2833638 NM_001669 exon6 c.G959A p.G320D exonic 0.99 D ---+--- 1 KIF21A kinesin family member 21A chr12 39727028 NM_001173463 exon17 c.C2434T p.R812C exonic 0.98 D +------ 1 GZF1 GDNF-inducible zinc finger protein 1 chr20 23350809 NM_022482 exon5 c.G1867A p.E623K exonic 0.98 D ---+--- 1 ANKRD20A2 ankyrin repeat domain 20 family, member A2 chr9 42396440 NM_001012419 exon11 c.A1054G p.R352G exonic 0.98 D +------ 1 ANKRD20A2 ankyrin repeat domain 20 family, member A2 chr9 43105400 NM_001012419 exon11 c.A1054G p.R352G exonic 0.98 D +------ 1 ATP6AP2 ATPase, H+ transporting, lysosomal accessory protein 2 chrX 40448358 NM_005765 exon2 c.C158T p.S53F exonic 0.97 D +------ 1 CCDC86 coiled-coil domain containing 86 chr11 60610178 NM_024098 exon1 c.A581T p.E194V exonic 0.97 D ---+--- 1 FCGBP Fc fragment of IgG binding protein chr19 40368666 NM_003890 exon28 c.C12682G p.Q4228E exonic 0.97 D -+-----