#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
KMT2D	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	49416133	49416133	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr12:49416133G>A	ENST00000301067.7	-	52	16341	c.16342C>T	c.(16342-16344)Cga>Tga	p.R5448*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5448	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TAGATGCCTCGATTCTAGAAA	0.517																																																0													46.0	44.0	45.0					12																	49416133		2075	4216	6291	SO:0001587	stop_gained	8085			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.16342C>T	12.37:g.49416133G>A	ENSP00000301067:p.Arg5448*		O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	56	27.258056	0.99971	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	.	.	.	5.11	4.21	0.49690	.	0.000000	0.29522	N	0.011916	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.4079	0.67096	0.0:0.0:0.8513:0.1487	.	.	.	.	X	5448;129	.	ENSP00000301067:R5448X	R	-	1	2	MLL2	47702400	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.634000	0.74290	1.280000	0.44463	0.650000	0.86243	CGA		0.517	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			9	11	9	11
BRCA2	675	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	32911765	32911765	+	Missense_Mutation	SNP	A	A	C	rs80359382|rs276174833		TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr13:32911765A>C	ENST00000380152.3	+	11	3506	c.3273A>C	c.(3271-3273)ttA>ttC	p.L1091F	BRCA2_ENST00000544455.1_Missense_Mutation_p.L1091F			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1091					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CTCAGATGTTATTTTCCAAGC	0.333			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	0													51.0	55.0	54.0					13																	32911765		2193	4287	6480	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3273A>C	13.37:g.32911765A>C	ENSP00000369497:p.Leu1091Phe		O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417750	0.25552	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.01152	5.26;5.26	5.45	0.269	0.15631	.	0.805067	0.10762	N	0.637052	T	0.03220	0.0094	M	0.77103	2.36	0.09310	N	1	P	0.45768	0.866	P	0.51742	0.678	T	0.35699	-0.9778	10	0.62326	D	0.03	.	4.1148	0.10076	0.5547:0.1734:0.2718:0.0	.	1091	P51587	BRCA2_HUMAN	F	1091	ENSP00000369497:L1091F;ENSP00000439902:L1091F	ENSP00000369497:L1091F	L	+	3	2	BRCA2	31809765	0.000000	0.05858	0.051000	0.19133	0.171000	0.22731	0.408000	0.21065	0.051000	0.15978	0.482000	0.46254	TTA		0.333	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		27	63	27	63
OR11H6	122748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	20692083	20692083	+	Missense_Mutation	SNP	G	G	A	rs201233405		TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr14:20692083G>A	ENST00000315519.2	+	1	293	c.215G>A	c.(214-216)cGg>cAg	p.R72Q		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	72						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TTGGACAGGCGGCTCCACACA	0.478													g|||	1	0.000199681	0.0	0.0	5008	,	,		18980	0.001		0.0	False		,,,				2504	0.0															0								G	GLN/ARG	0,4406		0,0,2203	120.0	110.0	113.0		215	-5.7	0.0	14		113	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR11H6	NM_001004480.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	72/331	20692083	1,13005	2203	4300	6503	SO:0001583	missense	122748				CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.215G>A	14.37:g.20692083G>A	ENSP00000319071:p.Arg72Gln		Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.30	1.311061	0.23821	0.0	1.16E-4	ENSG00000176219	ENST00000315519	T	0.00583	6.41	4.77	-5.71	0.02413	GPCR, rhodopsin-like superfamily (1);	1.552910	0.04597	N	0.397761	T	0.00875	0.0029	L	0.58101	1.795	0.09310	N	1	B	0.18968	0.032	B	0.15870	0.014	T	0.36311	-0.9753	10	0.44086	T	0.13	.	14.8461	0.70261	0.8184:0.0:0.1816:0.0	.	72	Q8NGC7	O11H6_HUMAN	Q	72	ENSP00000319071:R72Q	ENSP00000319071:R72Q	R	+	2	0	OR11H6	19761923	0.000000	0.05858	0.001000	0.08648	0.785000	0.44390	-2.149000	0.01291	-1.136000	0.02892	-0.417000	0.06048	CGG		0.478	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			22	88	22	88
GPATCH2L	55668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	76668100	76668100	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr14:76668100G>A	ENST00000261530.7	+	10	1421	c.1355G>A	c.(1354-1356)tGg>tAg	p.W452*	GPATCH2L_ENST00000312858.5_Nonsense_Mutation_p.W447*|GPATCH2L_ENST00000556675.1_Intron	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	452																	AGCTCTGAGTGGTTGGTGAGG	0.488																																																0													94.0	89.0	91.0					14																	76668100		2203	4300	6503	SO:0001587	stop_gained	55668			AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 118"""	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.1355G>A	14.37:g.76668100G>A	ENSP00000261530:p.Trp452*		B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Nonsense_Mutation	SNP	ENST00000261530.7	37	CCDS9848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.6|22.6	4.310838|4.310838	0.81358|0.81358	.|.	.|.	ENSG00000089916|ENSG00000089916	ENST00000336993|ENST00000312858;ENST00000261530	.|.	.|.	.|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.075639	.|0.64402	.|D	.|0.000020	T|.	0.45478|.	0.1344|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34054|.	-0.9844|.	5|.	0.87932|0.02654	D|T	0|1	-12.4709|-12.4709	17.0917|17.0917	0.86624|0.86624	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|X	446|447;452	.|.	ENSP00000337200:G446S|ENSP00000261530:W452X	G|W	+|+	1|2	0|0	C14orf118|C14orf118	75737853|75737853	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.344000|0.344000	0.29017|0.29017	5.758000|5.758000	0.68776|0.68776	2.715000|2.715000	0.92844|0.92844	0.655000|0.655000	0.94253|0.94253	GGT|TGG		0.488	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		14	60	14	60
INF2	64423	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	105174321	105174321	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr14:105174321C>T	ENST00000392634.4	+	8	1829	c.1717C>T	c.(1717-1719)Cca>Tca	p.P573S	INF2_ENST00000330634.7_Missense_Mutation_p.P573S	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	573	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GCAGAAGCTGCCATCCAACGT	0.657																																																0													39.0	43.0	42.0					14																	105174321		2116	4209	6325	SO:0001583	missense	64423			AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1717C>T	14.37:g.105174321C>T	ENSP00000376410:p.Pro573Ser		Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	.	.	.	.	.	.	.	.	.	.	C	13.75	2.329821	0.41297	.	.	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.17054	2.3;2.3	4.04	4.04	0.47022	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.201782	0.43416	U	0.000577	T	0.31009	0.0783	M	0.71581	2.175	0.80722	D	1	P;P	0.47841	0.879;0.901	P;P	0.49332	0.472;0.607	T	0.25047	-1.0143	10	0.66056	D	0.02	.	16.1904	0.81986	0.0:1.0:0.0:0.0	.	573;573	Q27J81-2;Q27J81	.;INF2_HUMAN	S	573	ENSP00000376406:P573S;ENSP00000376410:P573S	ENSP00000252527:P41S	P	+	1	0	INF2	104245366	1.000000	0.71417	0.871000	0.34182	0.010000	0.07245	5.101000	0.64566	1.780000	0.52325	0.491000	0.48974	CCA		0.657	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		20	38	20	38
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000540499.2_Missense_Mutation_p.R120K|IDH2_ENST00000559482.1_Intron|IDH2_ENST00000539790.1_Missense_Mutation_p.R42K	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)											85.0	81.0	82.0					15																	90631838		2200	4298	6498	SO:0001583	missense	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	15.37:g.90631838C>T	ENSP00000331897:p.Arg172Lys		B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			22	57	22	57
ABCA8	10351	hgsc.bcm.edu;broad.mit.edu	37	17	66914237	66914237	+	Silent	SNP	G	G	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr17:66914237G>A	ENST00000269080.2	-	14	2015	c.1878C>T	c.(1876-1878)cgC>cgT	p.R626R	ABCA8_ENST00000430352.2_Silent_p.R666R|ABCA8_ENST00000586539.1_Silent_p.R666R	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	626	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					AGAGGATCACGCGGTCTGTTT	0.453																																																0													192.0	151.0	165.0					17																	66914237		2203	4300	6503	SO:0001819	synonymous_variant	10351			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.1878C>T	17.37:g.66914237G>A			A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																				0.453	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		7	80	7	80
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42791757	42791757	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr19:42791757C>T	ENST00000575354.2	+	5	683	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	CIC_ENST00000160740.3_Missense_Mutation_p.R215W|CIC_ENST00000572681.2_Missense_Mutation_p.R1124W	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R215W(4)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CAAGCGGCACCGGGCCCTGGT	0.612			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	4	Substitution - Missense(4)	central_nervous_system(4)											64.0	64.0	64.0					19																	42791757		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.643C>T	19.37:g.42791757C>T	ENSP00000458663:p.Arg215Trp		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199892	0.58126	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.39	4.39	0.52855	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.82033	0.4949	M	0.93241	3.395	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.85234	0.1034	8	0.87932	D	0	-14.3323	9.6958	0.40156	0.2069:0.7931:0.0:0.0	.	215	Q96RK0	CIC_HUMAN	W	215	.	ENSP00000160740:R215W	R	+	1	2	CIC	47483597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.293000	0.59037	2.284000	0.76573	0.555000	0.69702	CGG		0.612	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			18	40	18	40
ZNF687	57592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	151258917	151258917	+	Silent	SNP	A	A	G			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr1:151258917A>G	ENST00000368879.2	+	2	248	c.150A>G	c.(148-150)gaA>gaG	p.E50E		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TAGGAAGTGAATCTGAAGACA	0.572																																																0													58.0	63.0	62.0					1																	151258917		2203	4300	6503	SO:0001819	synonymous_variant	57592				CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.150A>G	1.37:g.151258917A>G			D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	37																																																																																					0.572	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		32	53	32	53
RNPEP	6051	hgsc.bcm.edu;broad.mit.edu	37	1	201966606	201966606	+	Silent	SNP	C	C	T	rs570330224		TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr1:201966606C>T	ENST00000295640.4	+	5	1057	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N	RP11-465N4.5_ENST00000608886.1_RNA|RNPEP_ENST00000471105.1_3'UTR|RP11-465N4.4_ENST00000415582.1_RNA|RNPEP_ENST00000367286.3_Silent_p.N299N|RP11-465N4.4_ENST00000419190.1_RNA	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	338					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TGGTCACCAACGCCAACTGGG	0.547													C|||	1	0.000199681	0.0	0.0	5008	,	,		18133	0.0		0.0	False		,,,				2504	0.001				GBM(19;39 479 7473 13131 19462)											0													117.0	101.0	107.0					1																	201966606		2203	4300	6503	SO:0001819	synonymous_variant	6051			BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.1014C>T	1.37:g.201966606C>T			Q9BVM9|Q9H1D4|Q9NPT7	Silent	SNP	ENST00000295640.4	37	CCDS1418.1																																																																																				0.547	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		6	101	6	101
IL2RB	3560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	37524372	37524372	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr22:37524372G>A	ENST00000216223.5	-	10	1618	c.1420C>T	c.(1420-1422)Cct>Tct	p.P474S		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	474					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GGGGTGGGAGGCCCCAGGGGC	0.677																																																0													16.0	21.0	19.0					22																	37524372		2122	4156	6278	SO:0001583	missense	3560			M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"""Interleukins and interleukin receptors"", ""CD molecules"""	6009	protein-coding gene	gene with protein product		146710	"""interleukin 15 receptor, beta"""	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1420C>T	22.37:g.37524372G>A	ENSP00000216223:p.Pro474Ser		B2R765	Missense_Mutation	SNP	ENST00000216223.5	37	CCDS13942.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.539375	0.27475	.	.	ENSG00000100385	ENST00000216223	T	0.08720	3.06	4.02	-0.864	0.10666	.	9.025830	0.00481	N	0.000121	T	0.08582	0.0213	L	0.51422	1.61	0.09310	N	1	B	0.30937	0.301	B	0.30572	0.117	T	0.25745	-1.0123	10	0.28530	T	0.3	0.0371	2.008	0.03481	0.1801:0.1556:0.504:0.1604	.	474	P14784	IL2RB_HUMAN	S	474	ENSP00000216223:P474S	ENSP00000216223:P474S	P	-	1	0	IL2RB	35854318	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.143000	0.16115	-0.149000	0.11215	-0.176000	0.13171	CCT		0.677	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1			23	45	23	45
SYAP1	94056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	16774794	16774794	+	Silent	SNP	C	C	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chrX:16774794C>A	ENST00000380155.3	+	7	826	c.733C>A	c.(733-735)Cgg>Agg	p.R245R		NM_032796.3	NP_116185.2	Q96A49	SYAP1_HUMAN	synapse associated protein 1	245						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(3)|lung(4)|pancreas(1)|prostate(1)|skin(1)	10	Hepatocellular(33;0.0997)					AGAGGCAGTACGGCCCAAAAC	0.343																																																0													82.0	75.0	77.0					X																	16774794		2203	4300	6503	SO:0001819	synonymous_variant	94056			AF338728	CCDS14177.1	Xp22.31	2010-06-25	2010-06-25		ENSG00000169895	ENSG00000169895			16273	protein-coding gene	gene with protein product	"""SAP47 homolog (Drosophila)"""					11483580	Standard	NM_032796		Approved	FLJ14495, PRO3113	uc004cxp.3	Q96A49	OTTHUMG00000021192	ENST00000380155.3:c.733C>A	X.37:g.16774794C>A			Q68CP1|Q96C60|Q96JQ6|Q96T20	Silent	SNP	ENST00000380155.3	37	CCDS14177.1																																																																																				0.343	SYAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055904.1	NM_032796		10	44	10	44
MORF4L2	9643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	102931856	102931856	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chrX:102931856T>C	ENST00000441076.2	-	4	404	c.100A>G	c.(100-102)Atg>Gtg	p.M34V	MORF4L2_ENST00000422154.2_Missense_Mutation_p.M34V|MORF4L2_ENST00000492116.1_5'UTR|MORF4L2_ENST00000451301.1_Missense_Mutation_p.M34V|MORF4L2_ENST00000423833.2_Missense_Mutation_p.M34V|MORF4L2_ENST00000360458.1_Missense_Mutation_p.M34V|MORF4L2_ENST00000433176.2_Missense_Mutation_p.M34V	NM_001142419.1|NM_012286.2	NP_001135891.1|NP_036418.1	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	34					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA repair (GO:0006281)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)	13						GCCCCTCTCATTTTACTTCTC	0.488																																																0													73.0	73.0	73.0					X																	102931856		2203	4300	6503	SO:0001583	missense	9643			AF100620	CCDS14512.1	Xq22	2010-11-24			ENSG00000123562	ENSG00000123562			16849	protein-coding gene	gene with protein product	"""MORF-related gene X"""	300409				9891081, 7584026	Standard	NM_012286		Approved	KIAA0026, MRGX	uc011msa.2	Q15014	OTTHUMG00000022104	ENST00000441076.2:c.100A>G	X.37:g.102931856T>C	ENSP00000391969:p.Met34Val		B3KP92|D3DXA5|Q567V0|Q8J026	Missense_Mutation	SNP	ENST00000441076.2	37	CCDS14512.1	.	.	.	.	.	.	.	.	.	.	T	9.723	1.160282	0.21454	.	.	ENSG00000123562	ENST00000360458;ENST00000433176;ENST00000422154;ENST00000451301;ENST00000441076;ENST00000423833;ENST00000434230;ENST00000418819;ENST00000442614;ENST00000422355	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	4.43	4.43	0.53597	.	0.079337	0.85682	D	0.000000	T	0.19604	0.0471	N	0.24115	0.695	0.50632	D	0.999885	B	0.25312	0.123	B	0.20184	0.028	T	0.05733	-1.0867	10	0.29301	T	0.29	-2.6251	10.9547	0.47351	0.0:0.0:0.0:1.0	.	34	Q15014	MO4L2_HUMAN	V	34	ENSP00000353643:M34V;ENSP00000415476:M34V;ENSP00000394417:M34V;ENSP00000410532:M34V;ENSP00000391969:M34V;ENSP00000416120:M34V	ENSP00000353643:M34V	M	-	1	0	MORF4L2	102818512	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.850000	0.62889	1.951000	0.56629	0.486000	0.48141	ATG		0.488	MORF4L2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057732.1	NM_012286		52	61	52	61
AFF2	2334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	148049222	148049222	+	Splice_Site	SNP	G	G	T			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chrX:148049222G>T	ENST00000370460.2	+	15	3746	c.3267G>T	c.(3265-3267)ctG>ctT	p.L1089L	AFF2_ENST00000370457.5_Splice_Site_p.L1054L|AFF2_ENST00000286437.5_Splice_Site_p.L730L|AFF2_ENST00000342251.3_Splice_Site_p.L1056L	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1089					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					CTGATGCACTGGTAAGTTTCC	0.348																																																0													155.0	140.0	145.0					X																	148049222		2203	4300	6503	SO:0001630	splice_region_variant	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3267+1G>T	X.37:g.148049222G>T			A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Splice_Site	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																				0.348	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	Silent	20	49	20	49
SAMD4A	23034	broad.mit.edu;hgsc.bcm.edu	37	14	55236839	55236840	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HT-7681-01A-11D-2395-08	TCGA-HT-7681-10C-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	378982db-a5b2-405d-be34-30b870c8d215	16689ce9-1a6c-4702-91eb-68955024ac3e	g.chr14:55236839_55236840insA	ENST00000554335.1	+	9	2277_2278	c.1614_1615insA	c.(1615-1617)aaafs	p.K539fs	SAMD4A_ENST00000251091.5_Frame_Shift_Ins_p.K451fs|SAMD4A_ENST00000555192.1_Frame_Shift_Ins_p.K130fs|SAMD4A_ENST00000357634.3_Frame_Shift_Ins_p.K538fs|SAMD4A_ENST00000392067.3_Frame_Shift_Ins_p.K539fs			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	539					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CAGAGACACAGAAAAAAAGATT	0.416																																																0																																										SO:0001589	frameshift_variant	23034			AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1621dupA	14.37:g.55236846_55236846dupA	ENSP00000452535:p.Lys539fs		A8MPZ5|Q0VA96|Q6PEW4	Frame_Shift_Ins	INS	ENST00000554335.1	37	CCDS32084.2																																																																																				0.416	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		26	99	26	99
