isoform_overrides_at_mskcc_grch37.txt

gene_name	refseq_id	enst_id	note
IKZF1	NM_006060.4	ENST00000331340.3	
RECQL4	NM_004260.3	ENST00000428558.2	
APC	NM_000038.5	ENST00000257430.4	
AR	NM_000044.3	ENST00000374690.3	
ATM	NM_000051.3	ENST00000278616.4	
BLM	NM_000057.2	ENST00000355112.3	
BRCA2	NM_000059.3	ENST00000380152.3	
BTK	NM_000061.2	ENST00000308731.7	
CDK4	NM_000075.3	ENST00000257904.6	
CYP19A1	NM_000103.3	ENST00000260433.2	
ERCC3	NM_000122.1	ENST00000285398.2	
ERCC5	NM_000123.3	ENST00000355739.4	
FANCA	NM_000135.2	ENST00000389301.3	
FANCC	NM_000136.2	ENST00000289081.3	
FGFR2	NM_000141.4	ENST00000358487.5	
FGFR3	NM_000142.4	ENST00000260795.2	
FH	NM_000143.3	ENST00000366560.3	
MSH6	NM_000179.2	ENST00000234420.5	
INSR	NM_000208.2	ENST00000302850.5	
JAK3	NM_000215.3	ENST00000458235.1	
KIT	NM_000222.2	ENST00000288135.5	
MET	NM_000245.2	ENST00000397752.3	
MITF	NM_000248.3	ENST00000394351.3	
MLH1	NM_000249.3	ENST00000231790.2	
MSH2	NM_000251.2	ENST00000233146.2	
PTCH1	NM_000264.3	ENST00000331920.6	
NF1	NM_000267.3	ENST00000356175.3	
NF2	NM_000268.3	ENST00000338641.4	
PTEN	NM_000314.4	ENST00000371953.3	
RB1	NM_000321.2	ENST00000267163.4	
SOX9	NM_000346.3	ENST00000245479.2	
TSC1	NM_000368.4	ENST00000298552.3	
TSHR	NM_000369.2	ENST00000298171.2	
ERCC2	NM_000400.3	ENST00000391945.4	
IFNGR1	NM_000416.2	ENST00000367739.4	
NOTCH3	NM_000435.2	ENST00000263388.2	
STK11	NM_000455.4	ENST00000326873.7	
TEK	NM_000459.3	ENST00000380036.4	
BARD1	NM_000465.2	ENST00000260947.4	
ALB	NM_000477.5	ENST00000295897.4	
ATRX	NM_000489.3	ENST00000373344.5	
GNAS	NM_000516.4	ENST00000371085.3	
PMS1	NM_000534.4	ENST00000441310.2	
PMS2	NM_000535.5	ENST00000265849.7	
HNF1A	NM_000545.5	ENST00000257555.6	identical to clinical transcript
TP53	NM_000546.5	ENST00000269305.4	
TSC2	NM_000548.3	ENST00000219476.3	
VHL	NM_000551.3	ENST00000256474.2	
IL10	NM_000572.2	ENST00000423557.1	
TAP1	NM_000593.5	ENST00000354258.4	
HGF	NM_000601.4	ENST00000222390.5	
BCL2	NM_000633.2	ENST00000333681.4	
CSF3R	NM_000760.3	ENST00000361632.4	
IGF1R	NM_000875.3	ENST00000268035.6	
PGR	NM_000926.4	ENST00000325455.5	
RARA	NM_000964.3	ENST00000254066.5	
SMAD2	NM_001003652.3	ENST00000262160.6	
MAPKAP1	NM_001006617.1	ENST00000265960.3	
SPOP	NM_001007228.1	ENST00000347630.2	
NTRK3	NM_001012338.2	ENST00000360948.2	
H3-5	NM_001013699.2	ENST00000340398.3	
AKT1	NM_001014431.1	ENST00000349310.3	
CD276	NM_001024736.1	ENST00000318443.5	
MYCL	NM_001033082.2	ENST00000397332.2	
BABAM1	NM_001033549.1	ENST00000359435.4	
CD79B	NM_001039933.1	ENST00000392795.3	
CYLD	NM_001042355.1	ENST00000398568.2	
NSD2	NM_001042424.2	ENST00000382891.5	known as WHSC1
KDM5A	NM_001042603.1	ENST00000399788.2	
STAG2	NM_001042749.1	ENST00000218089.9	
NKX2-1	NM_001079668.2	ENST00000354822.5	
CASP8	NM_001080125.1	ENST00000358485.4	
CMTR2	NM_001099642.1	ENST00000338099.5	known as FTSJD1
INPP4B	NM_001101669.1	ENST00000262992.4	
SLFN11	NM_001104589.1	ENST00000308377.4	
ACVR1	NM_001111067.2	ENST00000263640.3	
IGF1	NM_001111285.1	ENST00000307046.8	
ESR1	NM_001122740.1	ENST00000206249.3	
H3C13	NM_001123375.2	ENST00000331491.1	
BCOR	NM_001123385.1	ENST00000378444.4	
TET2	NM_001127208.2	ENST00000380013.4	
BBC3	NM_001127240.2	ENST00000449228.1	
MAD2L2	NM_001127325.1	ENST00000235310.3	
IGF2	NM_001127598.1	ENST00000434045.2	
MUTYH	NM_001128425.1	ENST00000450313.1	Germline clinical transcript In HG38, it will be ENST00000710952, which has the same sequence as ENST00000450313 and it's also selected as MANE plus clinical
SMARCA4	NM_001128849.1	ENST00000358026.2	
YAP1	NM_001130145.2	ENST00000282441.5	
EIF4E	NM_001130678.1	ENST00000280892.6	
INPP4A	NM_001134224.1	ENST00000074304.5	
GRIN2A	NM_001134407.1	ENST00000330684.3	
TMPRSS2	NM_001135099.1	ENST00000398585.3	
TCF3	NM_001136139.2	ENST00000344749.5	
ALOX12B	NM_001139.2	ENST00000319144.4	
DAXX	NM_001141970.1	ENST00000374542.5	
TP53BP1	NM_001141980.1	ENST00000382044.4	
RAD54L	NM_001142548.1	ENST00000371975.4	
SCG5	NM_001144757.1	ENST00000300175.4	
CDK6	NM_001145306.1	ENST00000265734.4	
SETDB1	NM_001145415.1	ENST00000271640.5	
MEF2B	NM_001145785.1	ENST00000162023.5	
TCF7L2	NM_001146274.1	ENST00000543371.1	
ETV1	NM_001163147.1	ENST00000405192.2	
MGA	NM_001164273.1	ENST00000219905.7	
XIAP	NM_001167.3	ENST00000355640.3	
SMYD3	NM_001167740.1	ENST00000388985.4	identical to clinical transcript
WWTR1	NM_001168280.1	ENST00000360632.3	
VEGFA	NM_001171623.1	ENST00000523873.1	identical to clinical transcript
FGFR1	NM_001174067.1	ENST00000425967.3	
ATXN7	NM_001177387.1	ENST00000398590.3	this transcript is longer, and this is not a clinical germline transcript,  it does not change any of the curated oncokb mutations, since they are all around the 30-43aa range
ATR	NM_001184.3	ENST00000350721.4	
REST	NM_001193508.1	ENST00000309042.7	
KMT2A	NM_001197104.1	ENST00000534358.1	
PRDM1	NM_001198.3	ENST00000369096.4	
NADK	NM_001198994.1	ENST00000378625.1	this is not a clinical germline transcript
RBM10	NM_001204468.1	ENST00000377604.3	Variants on Mpath dont seem to map to any of the reported transcript. Mpath uses NM_001204468, its 93% similar to ENST00000377604 but not same. MANE Transcript but not aligning to listed clinical transcript.
ZNRF3	NM_001206998.1	ENST00000544604.2	
CCNE1	NM_001238.2	ENST00000262643.3	
HLA-A	NM_001242758.1	ENST00000376809.5	
CSDE1	NM_001242891.1	ENST00000438362.2	
FOXP1	NM_001244814.1	ENST00000318789.4	
PGBD5	NM_001258311.1	ENST00000391860.1	Best matching protein is ENST00000321327 to clinical protein sequence, however it is not identical. Exclusive to Iv7_dmp_isoform_merged_overrides
CDK8	NM_001260.1	ENST00000381527.3	
CHEK1	NM_001274.5	ENST00000428830.2	
DNMT1	NM_001379.2	ENST00000340748.4	identical to clinical transcript
DUSP4	NM_001394.6	ENST00000240100.2	
EIF1AX	NM_001412.3	ENST00000379607.5	
EP300	NM_001429.3	ENST00000263253.7	
EPAS1	NM_001430.4	ENST00000263734.3	
FOXF1	NM_001451.2	ENST00000262426.4	
INPPL1	NM_001567.3	ENST00000298229.2	
PARP1	NM_001618.3	ENST00000366794.5	
AKT2	NM_001626.4	ENST00000392038.2	
ARAF	NM_001654.4	ENST00000377045.4	
RHOA	NM_001664.2	ENST00000418115.1	
BCL6	NM_001706.4	ENST00000232014.4	
KLF5	NM_001730.3	ENST00000377687.4	
RUNX1	NM_001754.4	ENST00000300305.3	
CCND2	NM_001759.3	ENST00000261254.3	
CCND3	NM_001760.3	ENST00000372991.4	
CD79A	NM_001783.3	ENST00000221972.3	
CDC42	NM_001791.3	ENST00000344548.3	
CENPA	NM_001809.3	ENST00000335756.4	
CTNNB1	NM_001904.3	ENST00000349496.5	
E2F3	NM_001949.4	ENST00000346618.3	
EIF4A2	NM_001967.3	ENST00000323963.5	identical to clinical transcript
ERBB3	NM_001982.3	ENST00000267101.3	
ETV6	NM_001987.4	ENST00000396373.4	
EZH1	NM_001991.3	ENST00000428826.2	identical to clinical transcript
FGF4	NM_002007.2	ENST00000168712.1	
FOXO1	NM_002015.3	ENST00000379561.5	
FLT1	NM_002019.4	ENST00000282397.4	
GATA1	NM_002049.3	ENST00000376670.3	
GATA3	NM_002051.2	ENST00000346208.3	identical to clinical transcript
GNA11	NM_002067.2	ENST00000078429.4	
GNAQ	NM_002072.3	ENST00000286548.4	
GNB1	NM_002074.3	ENST00000378609.4	
GSK3B	NM_002093.3	ENST00000316626.5	identical to clinical transcript
H3-3A	NM_002107.4	ENST00000366813.1	
HLA-C	NM_002117.5	ENST00000376228.5	
ID3	NM_002167.4	ENST00000374561.5	
IDH2	NM_002168.2	ENST00000330062.3	
IL7R	NM_002185.3	ENST00000303115.3	
INHA	NM_002191.3	ENST00000243786.2	
INHBA	NM_002192.2	ENST00000242208.4	
JAK1	NM_002227.2	ENST00000342505.4	
JUN	NM_002228.3	ENST00000371222.2	
KDR	NM_002253.2	ENST00000263923.4	
LMO1	NM_002315.2	ENST00000335790.3	
LYN	NM_002350.3	ENST00000519728.1	
SH2D1A	NM_002351.4	ENST00000371139.4	
EPCAM	NM_002354.2	ENST00000263735.4	
MAX	NM_002382.4	ENST00000358664.4	
MDM2	NM_002392.5	ENST00000462284.1	
MDM4	NM_002393.4	ENST00000367182.3	
MSH3	NM_002439.4	ENST00000265081.6	
MSI1	NM_002442.3	ENST00000257552.2	
MST1R	NM_002447.2	ENST00000296474.3	
MTAP	NM_002451.3	ENST00000380172.4	
IRF4	NM_002460.3	ENST00000380956.4	
MYC	NM_002467.4	ENST00000377970.2	
MYD88	NM_002468.4	ENST00000396334.3	
MYOD1	NM_002478.4	ENST00000250003.3	
NBN	NM_002485.4	ENST00000265433.3	
NPM1	NM_002520.6	ENST00000296930.5	
NRAS	NM_002524.4	ENST00000369535.4	
NTHL1	NM_002528.5	ENST00000219066.1	
NTRK1	NM_002529.3	ENST00000524377.1	
PAK1	NM_002576.4	ENST00000356341.3	
PDGFRB	NM_002609.3	ENST00000261799.4	
PDPK1	NM_002613.4	ENST00000342085.4	
PIK3C3	NM_002647.2	ENST00000262039.4	
PIM1	NM_002648.3	ENST00000373509.5	
PIK3CG	NM_002649.2	ENST00000359195.3	
PLCG2	NM_002661.3	ENST00000359376.3	
POLD1	NM_002691.3	ENST00000440232.2	
PPP6C	NM_002721.4	ENST00000373547.4	
PRKCI	NM_002740.5	ENST00000295797.4	
PRKD1	NM_002742.2	ENST00000331968.5	
MAPK1	NM_002745.4	ENST00000215832.6	
MAPK3	NM_002746.2	ENST00000263025.4	
MAP2K1	NM_002755.3	ENST00000307102.5	
PTPN11	NM_002834.3	ENST00000351677.2	
PTPRD	NM_002839.3	ENST00000356435.5	
PTPRS	NM_002850.3	ENST00000357368.4	
RAC2	NM_002872.4	ENST00000249071.6	
RAD51	NM_002875.4	ENST00000267868.3	
RAD51D	NM_002878.3	ENST00000345365.6	
RAF1	NM_002880.3	ENST00000251849.4	
RASA1	NM_002890.2	ENST00000274376.6	
RECQL	NM_002907.3	ENST00000421138.2	
REL	NM_002908.2	ENST00000295025.8	
UPF1	NM_002911.3	ENST00000262803.5	
ROS1	NM_002944.2	ENST00000368508.3	
RXRA	NM_002957.4	ENST00000481739.1	
SERPINB4	NM_002974.2	ENST00000341074.5	Exclusive to Iv7_dmp_isoform_merged_overrides
SDHB	NM_003000.2	ENST00000375499.3	
SDHC	NM_003001.3	ENST00000367975.2	
SDHD	NM_003002.3	ENST00000375549.3	
MAP2K4	NM_003010.3	ENST00000353533.5	
SRSF2	NM_003016.4	ENST00000359995.5	
SMARCA2	NM_003070.3	ENST00000349721.2	
SMARCB1	NM_003073.3	ENST00000263121.7	
SMARCD1	NM_003076.4	ENST00000394963.4	
SMARCE1	NM_003079.4	ENST00000348513.6	
SOX2	NM_003106.3	ENST00000325404.1	
STAT5A	NM_003152.3	ENST00000345506.4	
SYK	NM_003177.5	ENST00000375746.1	
TOP1	NM_003286.2	ENST00000361337.2	
XPO1	NM_003400.3	ENST00000401558.2	
PTP4A1	NM_003463.4	ENST00000370651.3	
CXCR4	NM_003467.2	ENST00000241393.3	
KMT2D	NM_003482.3	ENST00000301067.7	
H3-4	NM_003493.2	ENST00000366696.1	
AXIN1	NM_003502.3	ENST00000262320.3	
H3C1	NM_003529.2	ENST00000357647.3	
H3C4	NM_003530.4	ENST00000356476.2	
H3C3	NM_003531.2	ENST00000540144.1	
H3C6	NM_003532.2	ENST00000360408.1	
H3C11	NM_003533.2	ENST00000328488.2	
H3C8	NM_003534.2	ENST00000305910.3	
H3C12	NM_003535.2	ENST00000359303.2	
H3C10	NM_003536.2	ENST00000369163.2	
H3C2	NM_003537.3	ENST00000244661.2	
CUL3	NM_003590.4	ENST00000264414.4	
AURKA	NM_003600.2	ENST00000312783.6	
PPM1D	NM_003620.3	ENST00000305921.3	
PIK3R3	NM_003629.3	ENST00000262741.5	
TP63	NM_003722.4	ENST00000264731.3	
SOCS1	NM_003745.1	ENST00000332029.2	
IRS2	NM_003749.2	ENST00000375856.3	
EED	NM_003797.3	ENST00000263360.6	
TNFRSF14	NM_003820.2	ENST00000355716.4	
FUBP1	NM_003902.3	ENST00000370768.2	
BCL10	NM_003921.4	ENST00000370580.1	
PHOX2B	NM_003924.3	ENST00000226382.2	
RPS6KA4	NM_003942.2	ENST00000334205.4	
RPS6KB2	NM_003952.2	ENST00000312629.5	
B2M	NM_004048.2	ENST00000558401.1	
CDKN1B	NM_004064.3	ENST00000228872.4	
FLT3	NM_004119.2	ENST00000241453.7	
SDHA	NM_004168.2	ENST00000264932.6	
KDM5C	NM_004187.3	ENST00000375401.3	
STK19	NM_004197.1	ENST00000375331.2	
AURKB	NM_004217.3	ENST00000585124.1	
KLF4	NM_004235.4	ENST00000374672.4	
TRIP13	NM_004237.3	ENST00000166345.3	
ALK	NM_004304.4	ENST00000389048.3	
BMPR1A	NM_004329.2	ENST00000372037.3	
BRAF	NM_004333.4	ENST00000288602.6	
CALR	NM_004343.3	ENST00000316448.5	
CDH1	NM_004360.3	ENST00000261769.5	
CEBPA	NM_004364.3	ENST00000498907.2	
CREBBP	NM_004380.2	ENST00000262367.5	
ELF3	NM_004433.4	ENST00000359651.3	
EPHA5	NM_004439.5	ENST00000273854.3	
EPHA7	NM_004440.3	ENST00000369303.4	
EPHB1	NM_004441.4	ENST00000398015.3	
ERBB2	NM_004448.2	ENST00000269571.5	identical to clinical transcript
EZH2	NM_004456.4	ENST00000320356.2	
GPS2	NM_004489.4	ENST00000380728.2	
ARHGAP35	NM_004491.4	ENST00000404338.3	
FOXA1	NM_004496.3	ENST00000250448.2	
NOTCH4	NM_004557.3	ENST00000375023.3	
PRKN	NM_004562.2	ENST00000366898.1	
PIK3C2G	NM_004570.4	ENST00000266497.5	
TGFBR1	NM_004612.2	ENST00000374994.4	
AXIN2	NM_004655.3	ENST00000307078.5	
BAP1	NM_004656.3	ENST00000460680.1	
LATS1	NM_004690.3	ENST00000253339.5	
MAP3K13	NM_004721.4	ENST00000265026.3	
MAP3K14	NM_003954.3	ENST00000344686.2	
CDKN2B	NM_004936.3	ENST00000276925.6	
MTOR	NM_004958.3	ENST00000361445.4	
JAK2	NM_004972.3	ENST00000381652.3	
KRAS	NM_004985.3	ENST00000311936.3	
PDCD1	NM_005018.2	ENST00000334409.5	
PIK3CD	NM_005026.3	ENST00000377346.4	
PIK3R2	NM_005027.3	ENST00000222254.8	
ZRSR2	NM_005089.3	ENST00000307771.7	
FGF19	NM_005117.2	ENST00000294312.3	
MED12	NM_005120.2	ENST00000374080.3	identical to clinical transcript
USP8	NM_005154.3	ENST00000307179.4	
ABL1	NM_005157.4	ENST00000318560.5	
APLNR	NM_005161.4	ENST00000257254.3	
CBL	NM_005188.3	ENST00000264033.4	
CRKL	NM_005207.3	ENST00000354336.3	
CSF1R	NM_005211.3	ENST00000286301.3	
CTLA4	NM_005214.4	ENST00000302823.3	
EGFR	NM_005228.3	ENST00000275493.2	
EPHA3	NM_005233.5	ENST00000336596.2	
ERBB4	NM_005235.2	ENST00000342788.4	
ERCC4	NM_005236.2	ENST00000311895.7	
FAT1	NM_005245.3	ENST00000441802.2	
FGF3	NM_005247.2	ENST00000334134.2	
GLI1	NM_005269.2	ENST00000228682.2	
H1-2	NM_005319.3	ENST00000343677.2	
H3-3B	NM_005324.3	ENST00000254810.4	
HRAS	NM_005343.2	ENST00000451590.1	
SMAD4	NM_005359.5	ENST00000342988.3	
MPL	NM_005373.2	ENST00000372470.3	
MYCN	NM_005378.4	ENST00000281043.3	
XRCC2	NM_005431.1	ENST00000359321.1	
YES1	NM_005433.3	ENST00000314574.4	
AKT3	NM_005465.4	ENST00000263826.5	
SH2B3	NM_005475.2	ENST00000341259.2	
HLA-B	NM_005514.6	ENST00000412585.2	
IRS1	NM_005544.2	ENST00000305123.5	
MRE11	NM_005591.3	ENST00000323929.3	
RHEB	NM_005614.3	ENST00000262187.5	
SMO	NM_005631.4	ENST00000249373.3	
SOS1	NM_005633.3	ENST00000402219.2	
ELOC	NM_005648.3	ENST00000284811.8	
RAD50	NM_005732.3	ENST00000265335.6	identical to clinical transcript
IDH1	NM_005896.2	ENST00000345146.2	
SMAD3	NM_005902.3	ENST00000327367.4	
MAP3K1	NM_005921.1	ENST00000399503.3	
MLLT1	NM_005934.3	ENST00000252674.7	
ARID1A	NM_006015.4	ENST00000324856.7	
DNAJB1	NM_006145.1	ENST00000254322.2	
NFE2L2	NM_006164.4	ENST00000397062.3	
NKX3-1	NM_006167.3	ENST00000380871.4	
NTRK2	NM_006180.3	ENST00000277120.3	
DDR2	NM_006182.2	ENST00000367921.3	
PDGFRA	NM_006206.4	ENST00000257290.5	
PIK3CA	NM_006218.2	ENST00000263967.3	
PIK3CB	NM_006219.2	ENST00000289153.2	
POLE	NM_006231.2	ENST00000320574.5	
RAD21	NM_006265.2	ENST00000297338.2	
RRAS	NM_006270.3	ENST00000246792.3	
TNFAIP3	NM_006290.3	ENST00000237289.4	
NCOR1	NM_006311.3	ENST00000268712.3	
HOXB13	NM_006361.5	ENST00000290295.7	
ERF	NM_006494.2	ENST00000222329.4	
CTCF	NM_006565.3	ENST00000264010.4	
PLK2	NM_006622.3	ENST00000274289.3	
U2AF1	NM_006758.2	ENST00000291552.4	
LZTR1	NM_006767.3	ENST00000215739.8	
MALT1	NM_006785.3	ENST00000348428.3	
PNRC1	NM_006813.2	ENST00000336032.3	
RAB35	NM_006861.6	ENST00000229340.5	
ZFHX3	NM_006885.3	ENST00000268489.5	
DNMT3B	NM_006892.3	ENST00000328111.2	
RIT1	NM_006912.5	ENST00000368323.3	
SERPINB3	NM_006919.2	ENST00000283752.5	
CHEK2	NM_007194.3	ENST00000328354.6	
BRCA1	NM_007294.3	ENST00000357654.3	
SHOC2	NM_007373.3	ENST00000369452.4	
AGO2	NM_012154.3	ENST00000220592.5	
AGO1	NM_012199.2	ENST00000373204.4	known as EIF2C1
RYBP	NM_012234.5	ENST00000477973.2	
RRAS2	NM_012250.5	ENST00000256196.4	identical to clinical transcript
SF3B1	NM_012433.2	ENST00000335508.6	
STAT5B	NM_012448.3	ENST00000293328.3	
DROSHA	NM_013235.4	ENST00000344624.3	
ANKRD11	NM_013275.5	ENST00000301030.4	
GREM1	NM_013372.6	ENST00000300177.4	
IKBKE	NM_014002.3	ENST00000367120.3	
CD274	NM_014143.3	ENST00000381577.3	
SETD2	NM_014159.6	ENST00000409792.3	
PPP2R1A	NM_014225.5	ENST00000322088.6	
SESN1	NM_014454.2	ENST00000436639.2	
LATS2	NM_014572.2	ENST00000382592.4	
CTR9	NM_014633.3	ENST00000361367.2	
MDC1	NM_014641.2	ENST00000376406.3	
NUP93	NM_014669.4	ENST00000308159.5	
KMT2B	NM_014727.1	ENST00000222270.7	
DIS3	NM_014953.3	ENST00000377767.4	
SPEN	NM_015001.2	ENST00000375759.3	
CIC	NM_015125.3	ENST00000575354.2	
ICOSLG	NM_015259.4	ENST00000407780.3	identical to clinical transcript
ASXL1	NM_015338.5	ENST00000375687.4	
SUZ12	NM_015355.2	ENST00000322652.5	
POT1	NM_015450.2	ENST00000357628.3	
PPARG	NM_015869.4	ENST00000287820.6	
SUFU	NM_016169.3	ENST00000369902.3	
CDK12	NM_016507.2	ENST00000447079.4	
TBX3	NM_016569.3	ENST00000257566.3	
PAX5	NM_016734.2	ENST00000358127.4	
NOTCH1	NM_017617.3	ENST00000277541.6	
TENT5C	NM_017709.3	ENST00000369448.3	
RNF43	NM_017763.4	ENST00000407977.2	
SDHAF2	NM_017841.2	ENST00000301761.2	
TMEM127	NM_017849.3	ENST00000258439.3	
KBTBD4	NM_018095.4	ENST00000430070.2	this is not a clinical germline transcript
SHQ1	NM_018130.2	ENST00000325599.8	
ASXL2	NM_018263.4	ENST00000435504.4	identical to clinical
PBRM1	NM_018313.4	ENST00000394830.3	
TAP2	NM_018833.2	ENST00000374899.4	
RAC1	NM_018890.3	ENST00000356142.4	
ERRFI1	NM_018948.3	ENST00000377482.5	
ETAA1	NM_019002.3	ENST00000272342.5	
CYSLTR2	NM_020377.2	ENST00000282018.3	
KMT5A	NM_020382.3	ENST00000330479.4	
NFKBIA	NM_020529.2	ENST00000216797.5	
DCUN1D1	NM_020640.2	ENST00000292782.4	
ARID1B	NM_020732.3	ENST00000346085.5	
RPTOR	NM_020761.2	ENST00000306801.3	
RET	NM_020975.4	ENST00000355710.3	
MST1	NM_020998.3	ENST00000449682.2	
H3C7	NM_021018.2	ENST00000446824.2	
H3C14	NM_021059.2	ENST00000369158.1	
H2BC5	NM_021063.3	ENST00000289316.2	
PMAIP1	NM_021127.2	ENST00000316660.6	
TRAF2	NM_021138.3	ENST00000247668.2	
KDM6A	NM_021140.2	ENST00000377967.4	
AXL	NM_021913.4	ENST00000301178.4	
MCL1	NM_021960.4	ENST00000369026.2	
CRLF2	NM_022148.2	ENST00000400841.2	According to UCSC oncogenic mutation F232 matches ENST00000381566 and clinical transcript. ENST00000400841.2 has 255aa and ENST00000400841.8 has 371 aa. They are an 100% overlap but not exact match. ENST00000400841.8 has additional aminoacids on N terminal. ENST00000400841.8 is MANE select.  
RRAGC	NM_022157.3	ENST00000373001.3	
SOX17	NM_022454.3	ENST00000297316.4	
NSD1	NM_022455.4	ENST00000439151.2	
COP1	NM_022457.5	ENST00000367669.3	
DNMT3A	NM_022552.4	ENST00000264709.3	
CBFB	NM_022845.2	ENST00000412916.2	Identical to clinical transcript
NSD3	NM_023034.1	ENST00000317025.8	
FOXL2	NM_023067.3	ENST00000330315.3	
NOTCH2	NM_024408.3	ENST00000256646.2	
WT1	NM_024426.4	ENST00000332351.3	
PRDM14	NM_024504.3	ENST00000276594.2	
CDC73	NM_024529.4	ENST00000367435.3	
VTCN1	NM_024626.3	ENST00000369458.3	
PALB2	NM_024675.3	ENST00000261584.4	
PREX2	NM_024870.2	ENST00000288368.4	
PDCD1LG2	NM_025239.3	ENST00000397747.3	
TET1	NM_030625.2	ENST00000373644.4	
MAP2K2	NM_030662.3	ENST00000262948.5	
NUF2	NM_031423.3	ENST00000271452.3	
SESN2	NM_031459.4	ENST00000253063.3	
STK40	NM_032017.1	ENST00000373129.3	
SPRTN	NM_032018.5	ENST00000295050.7	Exclusive to Iv7_dmp_isoform_merged_overrides
BRIP1	NM_032043.2	ENST00000259008.2	
ARID5B	NM_032199.2	ENST00000279873.7	
TRAF7	NM_032271.2	ENST00000326181.6	
CARD11	NM_032415.4	ENST00000396946.4	
SLX4	NM_032444.2	ENST00000294008.3	
PHF6	NM_032458.2	ENST00000332070.3	
DOT1L	NM_032482.2	ENST00000398665.3	
GATA2	NM_032638.4	ENST00000341105.2	
RTEL1	NM_001283009.1	ENST00000360203.5	
KNSTRN	NM_033286.3	ENST00000249776.8	
FBXW7	NM_033632.3	ENST00000281708.4	
CCND1	NM_053056.2	ENST00000227507.2	
RAD51C	NM_058216.2	ENST00000337432.4	
BRD4	NM_058243.2	ENST00000263377.2	
CDKN1A	NM_078467.2	ENST00000244741.5	
CDKN2C	NM_078626.2	ENST00000262662.1	
GAB2	NM_080491.2	ENST00000361507.4	
MEN1	NM_130799.2	ENST00000312049.6	
PTPRT	NM_133170.3	ENST00000373198.4	
RAD51B	NM_133509.3	ENST00000487270.1	
RAD52	NM_134424.2	ENST00000358495.3	
BCL2L1	NM_138578.1	ENST00000307677.4	
BCL2L11	NM_138621.4	ENST00000393256.3	
MSI2	NM_138962.2	ENST00000284073.2	
ABRAXAS1	NM_139076.2	ENST00000321945.7	
STAT3	NM_139276.2	ENST00000264657.5	
SESN3	NM_144665.3	ENST00000536441.1	
FLCN	NM_144997.5	ENST00000285071.4	
CCNQ	NM_152274.4	ENST00000406277.2	known as FAM58A. This transcript is directly listed in their transcript list
AMER1	NM_152424.3	ENST00000330258.3	
SPRED1	NM_152594.2	ENST00000299084.4	
ARID2	NM_152641.2	ENST00000334344.6	
RICTOR	NM_152756.3	ENST00000357387.3	
FYN	NM_153047.3	ENST00000368678.4	
KMT2C	NM_170606.2	ENST00000262189.6	
NEGR1	NM_173808.2	ENST00000357731.5	
PPP4R2	NM_174907.2	ENST00000356692.5	identical to clinical transcript
DICER1	NM_177438.2	ENST00000393063.1	
PAK5	NM_177990.2	ENST00000353224.5	known as PAK7
PIK3R1	NM_181523.2	ENST00000274335.5	
NCOA3	NM_181659.2	ENST00000371998.3	identical to clinical transcript
ERG	NM_182918.3	ENST00000288319.7	
FLT4	NM_182925.4	ENST00000261937.6	
BIRC3	NM_182962.2	ENST00000263464.3	
TERT	NM_198253.2	ENST00000310581.5	
SRC	NM_198291.2	ENST00000358208.4	
CARM1	NM_199141.1	ENST00000327064.4	
EGFL7	NM_201446.2	ENST00000308874.7	
KEAP1	NM_203500.1	ENST00000171111.5	
GAB1	NM_207123.2	ENST00000262995.4	This is not a clinical germline transcript
PRKAR1A	NM_212471.2	ENST00000358598.2	
FGFR4	NM_213647.1	ENST00000292408.4	
TGFBR2	NM_003242.5	ENST00000295754.5	
CDKN2A	NM_058195.3	ENST00000579755.1	ENST00000579755.1 (p14) + ENST00000304494.5 (p16).  ENST00000579755 is MANE plus clinical p14, ENST00000304494 is (p16 MANE. Germline transcript is MANE plus clinical. This transcript matches in a lot of ways, however the germline transcript is shorter.
CDKN2A	NM_000077.4	ENST00000304494.5	ENST00000579755.1 (p14) + ENST00000304494.5 (p16).  ENST00000579755 is MANE plus clinical p14, ENST00000304494 is (p16 MANE. Germline transcript is MANE plus clinical. This transcript matches in a lot of ways, however the germline transcript is shorter.
BCL2L11	NM_138621.4	ENST00000393256.3	Targetted for structural variants only
NUTM1	NM_175741.1	ENST00000333756.4	should call NUT or NUTM1? Targetted for structural variants only
CD74	NM_001025159.2	ENST00000009530.7	Targetted for structural variants only
EWSR1	NM_013986.3	ENST00000397938.2	Targetted for structural variants only
NAB2	NM_005967.3	ENST00000300131.3	Targetted for structural variants only
PAX8	NM_003466.3	ENST00000429538.3	ENST00000429538 (MANE) Most closest to clinicalTargetted for structural variants only
RELA	NM_021975.3	ENST00000406246.3	Targetted for structural variants only
TFE3	NM_006521.4	ENST00000315869.7	Targetted for structural variants only
BIVM-ERCC5	NM_001204425.1	ENST00000602836.1	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
FIP1L1	NM_001134937.1	ENST00000358575.5	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
INSRR	NM_014215.2	ENST00000368195.3	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
PTDSS1	NM_014754.1	ENST00000517309.1	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
RNF34	NM_025126.3	ENST00000361234.5	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
SDCCAG8	NM_006642.3	ENST00000366541.3	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
TOE1	NM_025077.3	ENST00000372090.5	Exclusive to mskcc_isoform_overrides.txt in vcf2maf
WDR74	NM_018093.2	ENST00000529106.1	Exclusive to mskcc_isoform_overrides.txt in vcf2maf