CSP-2.3.1

CSP-2.3.1 Genes Targeted

The Kailos Genetics CSP (v2.3) Panel targets the coding regions and splice junctions for the following genes as defined by the union of RefSeq transcripts below.

Gene Symbol Transcripts APC NM_000038, NM_001127510 ATM NM_000051 BARD1 NM_000465, NM_001282543, NM_001282545, NM_001282548, NM_001282549, NR_104212, NR_104215, NR_104216 BMPR1A NM_004329 BRCA1 NM_007294, NM_007297, NM_007298, NM_007299, NM_007300, NR_027676 BRCA2 NM_000059 BRIP1 NM_032043 CDH1 NM_001317184, NM_001317185, NM_001317186, NM_004360 CDKN2A NM_001195132 CHEK2 NM_001005735, NM_001257387, NM_007194, NM_145862 EPCAM NM_002354 FH NM_000143 FLCN NM_144997 MLH1 NM_000249, NM_001167617, NM_001167618, NM_001167619, NM_001258271, NM_001258273, NM_001258274 MRE11A NM_001330347, NM_005590, NM_005591 MSH2 NM_000251, NM_001258281 MSH6 NM_000179, NM_001281492, NM_001281493, NM_001281494 MUTYH NM_001048171, NM_001048172, NM_001048173, NM_001048174, NM_001128425, NM_001293190, NM_001293191, NM_001293192, NM_001293195, NM_001293196, NM_012222 NBN NM_001024688, NM_002485 PALB2 NM_024675 PMS2 NM_000535, NM_001322003, NM_001322004, NM_001322005, NM_001322006, NM_001322007, NM_001322008, NM_001322009, NM_001322010, NM_001322011, NM_001322012, NM_001322013, NM_001322014, NM_001322015, NR_136154 PTEN NM_000314 RAD50 NM_005732 RAD51C NM_002876, NM_058216, NR_103872, NR_103873 RAD51D NM_001142571, NM_002878, NM_133629, NR_037711, NR_037712 RINT1 NM_001346599, NM_001346600, NM_001346601, NM_001346603, NM_021930, NR_144478 SDHB NM_003000 SMAD4 NM_005359 STK11 NM_000455 TP53 NM_000546, NM_001126112, NM_001126113, NM_001126114, NM_001126115, NM_001126116, NM_001126117, NM_001126118, NM_001276695, NM_001276696, NM_001276697, NM_001276698, NM_001276699, NM_001276760, NM_001276761 VHL NM_000551, NM_198156 XRCC2 NM_005431
CSP-2.3.1 Reportable Range

The Kailos Genetics CSP (v2.3) Panel will report any CLINVAR pathogenic or likely pathogenic variant found in the following regions.

Gene Symbol Range* APC chr5:112090542-112090779 APC chr5:112101946-112102187 APC chr5:112102843-112103147 APC chr5:112111241-112111302 APC chr5:112111325-112111519 APC chr5:112116405-112116668 APC chr5:112128118-112128332 APC chr5:112136939-112137081 APC chr5:112137125-112137167 APC chr5:112151119-112151330 APC chr5:112154580-112155103 APC chr5:112157504-112157759 APC chr5:112162736-112163007 APC chr5:112163541-112163724 APC chr5:112164472-112164682 APC chr5:112170616-112170878 APC chr5:112173143-112179897 ATM chr11:108098321-108098698 ATM chr11:108099826-108100066 ATM chr11:108106336-108106618 ATM chr11:108114564-108114655 ATM chr11:108114679-108114922 ATM chr11:108115495-108115773 ATM chr11:108117634-108117913 ATM chr11:108119736-108119878 ATM chr11:108121378-108121409 ATM chr11:108121426-108121804 ATM chr11:108122528-108122800 ATM chr11:108123451-108123731 ATM chr11:108124518-108124793 ATM chr11:108126820-108126893 ATM chr11:108126927-108127097 ATM chr11:108128132-108128410 ATM chr11:108129619-108129897 ATM chr11:108137845-108138123 ATM chr11:108139073-108139380 ATM chr11:108141713-108141897 ATM chr11:108142034-108142195 ATM chr11:108143193-108143641 ATM chr11:108150138-108150186 ATM chr11:108150214-108150397 ATM chr11:108151647-108151928 ATM chr11:108153398-108153678 ATM chr11:108154951-108155217 ATM chr11:108158246-108158285 ATM chr11:108158315-108158524 ATM chr11:108159628-108159890 ATM chr11:108160288-108160572 ATM chr11:108163973-108164008 ATM chr11:108164039-108164239 ATM chr11:108165590-108165859 ATM chr11:108167947-108168206 ATM chr11:108170388-108170668 ATM chr11:108172307-108172585 ATM chr11:108173529-108173805 ATM chr11:108175352-108175632 ATM chr11:108178529-108178807 ATM chr11:108180801-108181082 ATM chr11:108183042-108183321 ATM chr11:108186452-108186928 ATM chr11:108188064-108188206 ATM chr11:108188280-108188307 ATM chr11:108190614-108190866 ATM chr11:108191955-108192197 ATM chr11:108196015-108196293 ATM chr11:108196753-108197001 ATM chr11:108198309-108198568 ATM chr11:108199718-108199996 ATM chr11:108200906-108201184 ATM chr11:108202114-108202297 ATM chr11:108202543-108202825 ATM chr11:108203419-108203692 ATM chr11:108204533-108204799 ATM chr11:108205633-108205893 ATM chr11:108206491-108206716 ATM chr11:108213885-108214163 ATM chr11:108216455-108216692 ATM chr11:108217910-108218188 ATM chr11:108224411-108224639 ATM chr11:108225431-108225714 ATM chr11:108235738-108236016 ATM chr11:108236023-108236278 BARD1 chr2:215593369-215593754 BARD1 chr2:215595095-215595292 BARD1 chr2:215609698-215609934 BARD1 chr2:215610373-215610631 BARD1 chr2:215617088-215617123 BARD1 chr2:215617146-215617354 BARD1 chr2:215632149-215632436 BARD1 chr2:215633857-215634139 BARD1 chr2:215645200-215646350 BARD1 chr2:215656912-215657064 BARD1 chr2:215657199-215657260 BARD1 chr2:215661724-215661952 BARD1 chr2:215674131-215674316 BMPR1A chr10:88635720-88635932 BMPR1A chr10:88649774-88650039 BMPR1A chr10:88651796-88651850 BMPR1A chr10:88651882-88652014 BMPR1A chr10:88659492-88659946 BMPR1A chr10:88671930-88672208 BMPR1A chr10:88676867-88677112 BMPR1A chr10:88678826-88679328 BMPR1A chr10:88681242-88681511 BMPR1A chr10:88683059-88683546 BRCA1 chr17:41197596-41197874 BRCA1 chr17:41199551-41199754 BRCA1 chr17:41201076-41201269 BRCA1 chr17:41202968-41203246 BRCA1 chr17:41209002-41209220 BRCA1 chr17:41215271-41215509 BRCA1 chr17:41215789-41216069 BRCA1 chr17:41219530-41219768 BRCA1 chr17:41222919-41223286 BRCA1 chr17:41226304-41226582 BRCA1 chr17:41228421-41228703 BRCA1 chr17:41231245-41231497 BRCA1 chr17:41234368-41234646 BRCA1 chr17:41242866-41243144 BRCA1 chr17:41243338-41246976 BRCA1 chr17:41247762-41248079 BRCA1 chr17:41249189-41249483 BRCA1 chr17:41251706-41251984 BRCA1 chr17:41256124-41256356 BRCA1 chr17:41256790-41257074 BRCA1 chr17:41258373-41258651 BRCA1 chr17:41267661-41267838 BRCA1 chr17:41267860-41267909 BRCA1 chr17:41275974-41276227 BRCA2 chr13:32890473-32890751 BRCA2 chr13:32893194-32893478 BRCA2 chr13:32899143-32899333 BRCA2 chr13:32899356-32899424 BRCA2 chr13:32900164-32900468 BRCA2 chr13:32900542-32900821 BRCA2 chr13:32903463-32903748 BRCA2 chr13:32904973-32905211 BRCA2 chr13:32906382-32907552 BRCA2 chr13:32910366-32915348 BRCA2 chr13:32918604-32918832 BRCA2 chr13:32920856-32921142 BRCA2 chr13:32928953-32929462 BRCA2 chr13:32930512-32930795 BRCA2 chr13:32931844-32932117 BRCA2 chr13:32936604-32936884 BRCA2 chr13:32937242-32937720 BRCA2 chr13:32944449-32944727 BRCA2 chr13:32945026-32945307 BRCA2 chr13:32950729-32951007 BRCA2 chr13:32953415-32953682 BRCA2 chr13:32953830-32954108 BRCA2 chr13:32954115-32954361 BRCA2 chr13:32968817-32969087 BRCA2 chr13:32970969-32971247 BRCA2 chr13:32972270-32972966 BRIP1 chr17:59760552-59761505 BRIP1 chr17:59763120-59763587 BRIP1 chr17:59770693-59770968 BRIP1 chr17:59793243-59793425 BRIP1 chr17:59793456-59793531 BRIP1 chr17:59820296-59820567 BRIP1 chr17:59821744-59822012 BRIP1 chr17:59853702-59853982 BRIP1 chr17:59857562-59857785 BRIP1 chr17:59858145-59858423 BRIP1 chr17:59861569-59861847 BRIP1 chr17:59870885-59871163 BRIP1 chr17:59876422-59876707 BRIP1 chr17:59878586-59878864 BRIP1 chr17:59885722-59886224 BRIP1 chr17:59924383-59924661 BRIP1 chr17:59926415-59926699 BRIP1 chr17:59934369-59934657 BRIP1 chr17:59937074-59937352 BRIP1 chr17:59938730-59939008 CDH1 chr16:68771313-68771395 CDH1 chr16:68772138-68772375 CDH1 chr16:68835546-68835824 CDH1 chr16:68842260-68842538 CDH1 chr16:68842555-68842813 CDH1 chr16:68844030-68844317 CDH1 chr16:68845536-68845797 CDH1 chr16:68845995-68846209 CDH1 chr16:68847168-68847431 CDH1 chr16:68849401-68849679 CDH1 chr16:68853117-68853357 CDH1 chr16:68855877-68856155 CDH1 chr16:68857252-68857553 CDH1 chr16:68862003-68862281 CDH1 chr16:68863490-68863768 CDH1 chr16:68867167-68867445 CDKN2A chr9:21968634-21968837 CDKN2A chr9:21970876-21971270 CDKN2A chr9:21974592-21974870 CHEK2 chr22:29083714-29083992 CHEK2 chr22:29085024-29085302 CHEK2 chr22:29089924-29090202 CHEK2 chr22:29091016-29091365 CHEK2 chr22:29091641-29091925 CHEK2 chr22:29092789-29093071 CHEK2 chr22:29095757-29096018 CHEK2 chr22:29099413-29099654 CHEK2 chr22:29105924-29106154 CHEK2 chr22:29107802-29108065 CHEK2 chr22:29115295-29115560 CHEK2 chr22:29120900-29121155 CHEK2 chr22:29121176-29121432 CHEK2 chr22:29126393-29126561 CHEK2 chr22:29130302-29130724 EPCAM chr2:47600517-47600795 EPCAM chr2:47600928-47601206 EPCAM chr2:47602253-47602531 EPCAM chr2:47604046-47604324 EPCAM chr2:47605977-47606265 EPCAM chr2:47606858-47607045 EPCAM chr2:47607105-47607142 EPCAM chr2:47612169-47612436 EPCAM chr2:47613688-47613966 FH chr1:241661059-241661079 FH chr1:241661123-241661338 FH chr1:241663670-241663807 FH chr1:241665672-241665923 FH chr1:241667305-241667583 FH chr1:241669273-241669522 FH chr1:241671877-241672142 FH chr1:241675216-241675502 FH chr1:241676884-241677081 FH chr1:241680466-241680688 FH chr1:241682886-241683031 FLCN chr17:17118481-17118651 FLCN chr17:17120328-17120579 FLCN chr17:17122301-17122572 FLCN chr17:17124761-17124957 FLCN chr17:17125782-17126019 FLCN chr17:17127221-17127486 FLCN chr17:17129487-17129654 FLCN chr17:17131198-17131468 MLH1 chr3:37034967-37035179 MLH1 chr3:37035186-37035464 MLH1 chr3:37038016-37038294 MLH1 chr3:37042354-37042627 MLH1 chr3:37045790-37046068 MLH1 chr3:37048379-37048667 MLH1 chr3:37050212-37050490 MLH1 chr3:37053193-37053685 MLH1 chr3:37055840-37056118 MLH1 chr3:37058905-37059183 MLH1 chr3:37061734-37062017 MLH1 chr3:37067226-37067508 MLH1 chr3:37070230-37070488 MLH1 chr3:37081592-37081870 MLH1 chr3:37083652-37083917 MLH1 chr3:37088953-37089201 MLH1 chr3:37089915-37090193 MLH1 chr3:37090313-37090591 MLH1 chr3:37091913-37092191 MRE11A chr11:94153112-94153385 MRE11A chr11:94162978-94163019 MRE11A chr11:94163076-94163159 MRE11A chr11:94163185-94163239 MRE11A chr11:94168894-94169174 MRE11A chr11:94170245-94170517 MRE11A chr11:94178879-94179134 MRE11A chr11:94180356-94180634 MRE11A chr11:94189344-94189600 MRE11A chr11:94192519-94192796 MRE11A chr11:94193987-94194261 MRE11A chr11:94197203-94197481 MRE11A chr11:94200880-94201158 MRE11A chr11:94203584-94203857 MRE11A chr11:94204716-94204945 MRE11A chr11:94209388-94209655 MRE11A chr11:94211835-94212111 MRE11A chr11:94212745-94213023 MRE11A chr11:94219031-94219297 MRE11A chr11:94223928-94224204 MRE11A chr11:94225871-94226149 MSH2 chr2:47630340-47630525 MSH2 chr2:47635478-47635522 MSH2 chr2:47635562-47635815 MSH2 chr2:47637158-47637202 MSH2 chr2:47637228-47637592 MSH2 chr2:47639452-47639724 MSH2 chr2:47641447-47641558 MSH2 chr2:47641606-47641657 MSH2 chr2:47643363-47643641 MSH2 chr2:47656878-47657120 MSH2 chr2:47672603-47672879 MSH2 chr2:47690093-47690369 MSH2 chr2:47693751-47694011 MSH2 chr2:47698016-47698063 MSH2 chr2:47698085-47698284 MSH2 chr2:47702146-47702426 MSH2 chr2:47703463-47703747 MSH2 chr2:47705394-47705675 MSH2 chr2:47707784-47708068 MSH2 chr2:47709888-47710175 MSH6 chr2:48010366-48010579 MSH6 chr2:48017989-48018235 MSH6 chr2:48018316-48018344 MSH6 chr2:48022994-48023257 MSH6 chr2:48025646-48028374 MSH6 chr2:48030467-48030867 MSH6 chr2:48031969-48032246 MSH6 chr2:48032713-48032739 MSH6 chr2:48032754-48032974 MSH6 chr2:48033287-48033534 MSH6 chr2:48033562-48033831 MSH6 chr2:48033856-48033882 MSH6 chr2:48033917-48034047 MUTYH chr1:45794916-45795177 MUTYH chr1:45796076-45796298 MUTYH chr1:45796940-45797279 MUTYH chr1:45797302-45797561 MUTYH chr1:45797620-45798189 MUTYH chr1:45798236-45798532 MUTYH chr1:45798566-45798720 MUTYH chr1:45798743-45799026 MUTYH chr1:45799057-45799319 MUTYH chr1:45800000-45800243 MUTYH chr1:45805831-45805956 NBN chr8:90947587-90947856 NBN chr8:90949140-90949418 NBN chr8:90955399-90955687 NBN chr8:90958307-90958585 NBN chr8:90959945-90960225 NBN chr8:90965461-90965944 NBN chr8:90967396-90967871 NBN chr8:90970872-90971157 NBN chr8:90976580-90976816 NBN chr8:90982579-90982860 NBN chr8:90983337-90983584 NBN chr8:90990367-90990649 NBN chr8:90992897-90993181 NBN chr8:90993538-90993816 NBN chr8:90994878-90995088 NBN chr8:90995110-90995156 NBN chr8:90996783-90996933 PALB2 chr16:23614600-23615018 PALB2 chr16:23619120-23619398 PALB2 chr16:23625230-23625508 PALB2 chr16:23632602-23632880 PALB2 chr16:23634229-23634510 PALB2 chr16:23635234-23635511 PALB2 chr16:23637499-23637777 PALB2 chr16:23640434-23640698 PALB2 chr16:23640899-23641849 PALB2 chr16:23646105-23646141 PALB2 chr16:23646166-23647664 PALB2 chr16:23647715-23647727 PALB2 chr16:23649090-23649560 PMS2 chr7:6012800-6013272 PMS2 chr7:6017165-6017443 PMS2 chr7:6018213-6018416 PMS2 chr7:6022400-6022656 PMS2 chr7:6026568-6027294 PMS2 chr7:6029368-6029616 PMS2 chr7:6031507-6031785 PMS2 chr7:6035076-6035354 PMS2 chr7:6036924-6037056 PMS2 chr7:6037075-6037145 PMS2 chr7:6038684-6038829 PMS2 chr7:6038839-6038984 PMS2 chr7:6042037-6042315 PMS2 chr7:6043217-6043473 PMS2 chr7:6043507-6043697 PMS2 chr7:6043726-6043759 PMS2 chr7:6045454-6045732 PMS2 chr7:6048604-6048752 PTEN chr10:89623334-89623511 PTEN chr10:89624138-89624335 PTEN chr10:89653703-89653963 PTEN chr10:89685154-89685439 PTEN chr10:89690687-89690886 PTEN chr10:89692750-89693027 PTEN chr10:89711801-89712083 PTEN chr10:89717572-89717830 PTEN chr10:89720649-89720902 PTEN chr10:89725018-89725269 RAD50 chr5:131892965-131893243 RAD50 chr5:131894907-131895151 RAD50 chr5:131911406-131911684 RAD50 chr5:131914982-131915241 RAD50 chr5:131915517-131915773 RAD50 chr5:131923179-131923464 RAD50 chr5:131923555-131923835 RAD50 chr5:131924338-131924598 RAD50 chr5:131925297-131925546 RAD50 chr5:131926868-131927147 RAD50 chr5:131927549-131927787 RAD50 chr5:131930496-131930758 RAD50 chr5:131931245-131931523 RAD50 chr5:131938940-131939226 RAD50 chr5:131939536-131939814 RAD50 chr5:131940432-131940710 RAD50 chr5:131944223-131944269 RAD50 chr5:131944306-131944501 RAD50 chr5:131944716-131944902 RAD50 chr5:131944945-131945167 RAD50 chr5:131951650-131951916 RAD50 chr5:131953735-131954013 RAD50 chr5:131972784-131972976 RAD50 chr5:131973705-131973927 RAD50 chr5:131976292-131976570 RAD50 chr5:131977836-131978116 RAD51C chr17:56769909-56770176 RAD51C chr17:56772170-56772672 RAD51C chr17:56773998-56774278 RAD51C chr17:56780485-56780763 RAD51C chr17:56787198-56787433 RAD51C chr17:56798052-56798279 RAD51C chr17:56801310-56801570 RAD51C chr17:56809706-56809851 RAD51C chr17:56809869-56810014 RAD51C chr17:56811462-56811725 RAD51D chr17:33427852-33428130 RAD51D chr17:33428177-33428441 RAD51D chr17:33430169-33430647 RAD51D chr17:33433314-33433592 RAD51D chr17:33433935-33434215 RAD51D chr17:33434287-33434565 RAD51D chr17:33443828-33444106 RAD51D chr17:33445511-33445712 RAD51D chr17:33446109-33446300 RAD51D chr17:33446507-33446651 RINT1 chr7:105172641-105172919 RINT1 chr7:105173155-105173433 RINT1 chr7:105176965-105177237 RINT1 chr7:105182842-105183115 RINT1 chr7:105187345-105187583 RINT1 chr7:105187607-105187845 RINT1 chr7:105188940-105189221 RINT1 chr7:105190412-105190637 RINT1 chr7:105190682-105190960 RINT1 chr7:105195436-105195694 RINT1 chr7:105204148-105204426 RINT1 chr7:105205713-105206175 RINT1 chr7:105207541-105207809 SDHB chr1:17345291-17345539 SDHB chr1:17349025-17349293 SDHB chr1:17350382-17350652 SDHB chr1:17354230-17354368 SDHB chr1:17354403-17354457 SDHB chr1:17355038-17355289 SDHB chr1:17359459-17359707 SDHB chr1:17371244-17371459 SDHB chr1:17380437-17380569 SMAD4 chr18:48573400-48573670 SMAD4 chr18:48575047-48575294 SMAD4 chr18:48575541-48575798 SMAD4 chr18:48581143-48581396 SMAD4 chr18:48584403-48584665 SMAD4 chr18:48584693-48584835 SMAD4 chr18:48584872-48584933 SMAD4 chr18:48591740-48592003 SMAD4 chr18:48593363-48593617 SMAD4 chr18:48602943-48603227 SMAD4 chr18:48604602-48604855 STK11 chr19:1206740-1206974 STK11 chr19:1207302-1207348 STK11 chr19:1218358-1218597 STK11 chr19:1219304-1219433 STK11 chr19:1219455-1219488 STK11 chr19:1220612-1220776 STK11 chr19:1221183-1221394 STK11 chr19:1221912-1222068 STK11 chr19:1222925-1223149 STK11 chr19:1226426-1226612 TP53 chr17:7572902-7573031 TP53 chr17:7573873-7574081 TP53 chr17:7576467-7576703 TP53 chr17:7576814-7576959 TP53 chr17:7576986-7577188 TP53 chr17:7577452-7577637 TP53 chr17:7578095-7578600 TP53 chr17:7579275-7579610 TP53 chr17:7579672-7579775 TP53 chr17:7579822-7579957 VHL chr3:10183589-10183901 VHL chr3:10188170-10188398 VHL chr3:10191421-10191699 XRCC2 chr7:152345697-152346495 XRCC2 chr7:152357688-152357936 XRCC2 chr7:152373078-152373220

* Ranges shown in hg19 / GRCh37 coordinates

 

CSP-2.3.1 Regions Excluded

The Kailos Genetics CSP (v2.3) Panel will not report on the following coding regions.

Gene Symbol Regions Excluded* Exclusion Length (bp) ATM chr11:108119660-108119735 76 ATM chr11:108141978-108142033 56 ATM chr11:108163346-108163520 175 ATM chr11:108188207-108188248 42 BARD1 chr2:215657065-215657169 105 EPCAM chr2:47596645-47596720 76 EPCAM chr2:47607046-47607104 59 FH chr1:241663808-241663890 83 FLCN chr17:17116969-17117170 202 FLCN chr17:17118299-17118404 106 FLCN chr17:17119694-17119817 124 MLH1 chr3:37067128-37067225 98 MSH2 chr2:47630331-47630339 9 MSH2 chr2:47630526-47630541 16 MSH2 chr2:47635540-47635561 22 MSH2 chr2:47641408-47641446 39 MSH6 chr2:48010580-48010632 53 MSH6 chr2:48018236-48018262 27 MUTYH chr1:45796854-45796939 86 NBN chr8:90996753-90996782 30 PALB2 chr16:23652431-23652478 48 PMS2 chr7:6026390-6026567 178 PMS2 chr7:6038830-6038838 9 RAD51C chr17:56809852-56809868 17 RINT1 chr7:105192017-105192154 138 SMAD4 chr18:48586236-48586286 51 STK11 chr19:1206975-1207202 228 STK11 chr19:1220372-1220504 133 STK11 chr19:1220580-1220611 32 STK11 chr19:1223150-1223171 22 STK11 chr19:1226613-1226646 34 VHL chr3:10183532-10183588 57

* Regions shown in hg19 / GRCh37 coordinates

Note: These regions account for approximately 2% of the total protein coding region