LMM / emerge III Network Reference Sequences October 2016 LMM / emerge III Network Consensus Actionable Gene List *ACMG56 gene
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1 LMM / emerge III Network Consensus Actionable Gene List *ACMG56 gene ACTA2* Exon NM_ DSG2* Exon NM_ ACTC1* Exon NM_ DSP* Exon NM_ APC* Exon NM_ FBN1* Exon NM_ APC* Exon 01A NM_ GLA* Exon NM_ APOB* Exon NM_ GLA* Intron 04 (c g>a; c g>a) NM_ BMPR1A Exon NM_ HNF1A Exon NM_ BRCA1* Exon 02A-23A NM_ HNF1B Exon NM_ BRCA1* Exon 13 NM_ KCNE1 Exon 03 NM_ BRCA2* Exon NM_ KCNH2* Exon NM_ CACNA1A Exon NM_ KCNH2* Exon 01B NM_ CACNA1A Exon 37D NM_ KCNH2* Exon 09A NM_ CACNA1S* Exon NM_ KCNJ2 Exon 02 NM_ COL3A1* Exon NM_ KCNQ1* Exon NM_ KCNQ1* Exon 01A NM_ COL5A1 Exon NM_ COL5A1 Exon 64A NM_ LDLR* Exon NM_ DSC2* Exon NM_ LMNA* Exon NM_ DSC2* Exon 15A NM_ LMNA* Exon 01B NM_ DSC2* Exon 15B NM_ LMNA* Exon 13B NM_ Page 1 of 8
2 LMM / emerge III Network Consensus Actionable Gene List *ACMG56 gene MEN1* Exon NM_ PCSK9* Exon NM_ MLH1* Exon NM_ PKP2* Exon NM_ MSH2* Exon NM_ PMS2* Exon NM_ MSH6* Exon NM_ POLD1 Exon 02A NM_ POLD1 Exon NM_ MUTYH* Exon NM_ POLE Exon NM_ MYBPC3* Exon NM_ PRKAG2* Exon NM_ MYH11* Exon NM_ MYH11* Exon 42A NM_ PTEN* Exon NM_ MYH7* Exon NM_ RB1* Exon NM_ MYL2* Exon NM_ RET* Exon NM_ RET* Exon 19A NM_ MYL3* Exon NM_ RYR1* Exon NM_ MYLK* Exon NM_ RYR2* Exon NM_ NF2* Exon NM_ NF2* Exon 16B NM_ SCN5A* Exon NM_ NF2* Exon 16C NM_ SCN5A* Exon 06A NM_ OTC Exon NM_ SDHAF2* Exon NM_ PALB2 Exon NM_ SDHB* Exon NM_ Page 2 of 8
3 LMM / emerge III Network Consensus Actionable Gene List *ACMG56 gene SDHC* Exon NM_ TPM1* Exon 02A, 10A NM_ SDHC* Exon 05A NM_ TPM1* Exon 01A, 10B NM_ SDHD* Exon NM_ TSC1* Exon NM_ SMAD3* Exon NM_ TSC2* Exon NM_ SMAD3* Exon 01B NM_ VHL* Exon NM_ SMAD4 Exon NM_ WT1* Exon NM_ STK11* Exon NM_ WT1* Exon 01B NM_ TGFBR1* Exon NM_ TGFBR2* Exon NM_ TGFBR2* Exon 01A NM_ TMEM43* Exon NM_ TNNI3* Exon NM_ TNNT2* Exon NM_ TNNT2* Exon 04A NM_ TP53* Exon NM_ TP53* Exon 10A NM_ TP53* Exon 10B NM_ TPM1* Exon 01-09, 06A NM_ TPM1* Exon 06B, 10 NM_ Page 3 of 8
4 LMM / emerge III Network Consensus Actionable "SNV" List Gene/Build Transcript/Chr Region AA rsid ACADM NM_ c.997a>g p.lys333glu rs ALDOB NM_ c.360_363delcaaa p.asn120lysfsx32 rs BCKDHB NM_ c.548g>c p.arg183pro rs BCKDHB NM_ c.832g>a p.gly278ser rs BLM NM_ c.2207_2212delins p.tyr736leufsx5 rs (delinstagattc) CPT2 NM_ c.1239_1240delga p.lys414thrfsx7 rs (c.1238_1239delag) CYP21A2 NM_ c c>g p.? rs6467 F5 NM_ c.1601a p.gln534 rs6025 FAH NM_ c.782c>t p.pro261leu rs G6PC NM_ c.247c>t p.arg83cys rs HFE NM_ c.845g>a p.cys282tyr rs MEFV NM_ c.2177t>c p.val726ala rs MEFV NM_ c.2080a>g p.met694val rs MSH2* NM_ c.942+3a>t NA rs MSH2* We cannot exclude the presence of a variant in this location due to challenging sequence Page 4 of 8
5 Additional emerge III Network Reportable Genes Available to Sites (by specific request) ANGPTL3 Exon NM_ CHEK2 Exon 02B-15B NM_ ANGPTL4 Exon NM_ CHEK2 Exon 03 NM_ CORIN Exon NM_ ANK2 Exon NM_ CORIN Exon 14B NM_ ANK2 Exon 02B, 28B NM_ FLG Exon 02 NM_ APOA5 Exon NM_ Not covered Exon 03 NM_ APOC3 Exon NM_ GRM1 Exon NM_ GRM1 Exon 08B NM_ APOE Exon NM_ GRM2 Exon NM_ ATM Exon NM_ GRM5 Exon NM_ ATP1A2 Exon NM_ GRM7 Exon NM_ BMPR2 Exon NM_ GRM7 Exon 10A NM_ CACNA1B Exon NM_ GRM8 Exon NM_ GRM8 Exon 10A NM_ CACNA1C Exon NM_ CACNA1C Exon 08V, 42V NM_ IL33 Exon NM_ CACNA1C Exon 32C, 39C NM_ IL4 Exon NM_ CFH Exon NM_ CFH Exon 10A NM_ MC4R Exon 01 NM_ CFTR Exon NM_ MTHFR Exon NM_ CFTR Intron 12 (c a>g) NM_ CFTR Intron 22 (c c>t) NM_ Page 5 of 8
6 Additional emerge III Network Reportable Genes Available to Sites (by specific request) NTRK1 Exon NM_ TTR Exon NM_ NTRK1 Exon 01A, 02A NM_ PLTP Exon NM_ PON1 Exon NM_ TYK2 Exon NM_ UMOD Exon NM_ VDR Exon 01A, 02A, 03A NM_ SCN1A Exon NM_ VDR Exon NM_ SCN9A Exon NM_ SERPINA1 Exon NM_ SLC25A40 Exon NM_ SLC2A10 Exon NM_ TCF4 Exon NM_ TCF4 Exon 01D NM_ TCF4 Exon 01F NM_ TCF4 Exon 01G NM_ TCF4 Exon 01I NM_ TCF4 Exon 01K NM_ TCF4 Exon 09A NM_ TCIRG1 Exon NM_ TNF Exon NM_ TSLP Exon NM_ Page 6 of 8
7 Additional emerge III Network Reportable "SNVs" Available to Sites (by specific request) For a full list of positions genotyped, contact the LMM LMM / emerge III Network Reference Sequences Gene/Build Transcript/Chr Region AA rsid ABCC8 NM_ c g>a NA rs ADAMTS2 NM_ c.673c>t p.gln225x rs APOB NM_ c.10580g>a p.arg3527gln rs (p.arg3500gln) APOB NM_ c.10579c>t p.arg3527trp rs (p.arg3500trp) APOC3 NM_ c.179+1g>t NA rs APOC3 NM_ c.55+1g>a NA rs ARSA NM_ c.1136c>t p.pro379leu rs ASPA NM_ c.693c>a p.tyr231x rs ASPA NM_ c.854a>c p.glu285ala rs ATP7B NM_ c.2874c>a p.his958gln rs CARD9 NM_ c g>c NA rs CHD8 NM_ c.2875c>t p.gln959x rs CHD8 NM_ c.3172c>t p.arg1058x rs CLRN1 NM_ c.144t>g p.asn48lys rs COL4A5 NM_ c.5048g>a p.arg1683gln rs COL5A2 NM_ c _1928del p.? rs (delagggagc) COL5A2 NM_ c g>t NA rs COL5A2 NM_ c.3445g>c p.gly1149arg rs COQ4 NM_ c.718c>t p.arg240cys rs CPT2 NM_ c.1342t>c p.phe448leu rs CYP1B1 NM_ c.1103g>a p.arg368his rs CYP1B1 NM_ c.1159g>a p.glu387lys rs DHCR7 NM_ c.964-1g>c NA rs DHCR7 NM_ c.453g>a p.trp151x rs DHDDS NM_ c.124a>g p.lys42glu rs DLD NM_ c.685g>t p.gly229cys rs F11 NM_ c.403g>t p.glu135x rs F11 NM_ c.901t>c p.phe301leu rs FAM161A NM_ c.1355_1356delca p.thr452serfsx3 rs FANCC NM_ c.456+4a>t NA rs FKTN NM_ c.1167_1168insa p.phe390ilefsx14 rs (c.1167dup) Page 7 of 8
8 Additional emerge III Network Reportable "SNVs" Available to Sites (by specific request) For a full list of positions genotyped, contact the LMM LMM / emerge III Network Reference Sequences Gene/Build Transcript/Chr Region AA rsid GBA NM_ c.27+1g>a NA rs GJB2 NM_ c.101t>c p.met34thr rs HEXA NM_ c.1274_1277dup p.tyr427ilefsx5 rs (duptatc) HEXA NM_ c g>c NA rs HPS3 NM_ c g>a NA rs JAK2 NM_ c.1849g>a p.val617ile rs KCNE2 NM_ c.161t>c p.met54thr rs KCNE2 NM_ c.29c>t p.thr10met rs LRRK2 NM_ c.6055g>a p.gly2019ser rs MCOLN1 NM_ c.406-2a>g NA rs MEFV NM_ c.1105c>t p.pro369ser rs MEFV NM_ c.2084a>g p.lys695arg rs MEFV NM_ c.442g>c p.glu148gln rs MPL NM_ c.79+2t>a NA rs MTTP NM_ c.2593g>t p.gly865x rs PCDH15 NM_ c.733c>t p.arg245x rs PEX2 NM_ c.355c>t p.arg119x rs PHGDH NM_ c.1468g>a p.val490met rs PMM2 NM_ c.422g>a p.arg141his rs RTEL1 NM_ c g>a NA rs SLC1A4 NM_ c.766g>a p.glu256lys rs SMPD1 NM_ c.1493g>t p.arg498leu rs SMPD1 NM_ c.1829_1831delgcc p.arg610del rs SMPD1 NM_ c.911t>c p.leu304pro rs SMPD1 NM_ c.996delc p.phe333serfsx52 rs SPG7 NM_ c.1529c>t p.ala510val rs TERT NM_ c.1892g>a p.arg631gln rs TMEM216 NM_ c.218g>t p.arg73leu rs TOR1A NM_ c.907_909delgag p.glu303del rs (c.907_909del) Page 8 of 8
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