#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
ATAD1	84896	hgsc.bcm.edu;broad.mit.edu	37	10	89536119	89536119	+	Missense_Mutation	SNP	T	T	G			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr10:89536119T>G	ENST00000308448.7	-	6	1027	c.649A>C	c.(649-651)Atg>Ctg	p.M217L	ATAD1_ENST00000400215.3_Missense_Mutation_p.M159L|ATAD1_ENST00000541004.1_Missense_Mutation_p.M217L|ATAD1_ENST00000328142.3_Missense_Mutation_p.M217L	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	217					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		CAGAGACTCATAAACTGAGCT	0.378																																																0													138.0	139.0	139.0					10																	89536119		2203	4300	6503	SO:0001583	missense	84896			AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"""ATPases / AAA-type"""	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.649A>C	10.37:g.89536119T>G	ENSP00000339017:p.Met217Leu		D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Missense_Mutation	SNP	ENST00000308448.7	37	CCDS7386.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.818826	0.90873	.	.	ENSG00000138138	ENST00000308448;ENST00000328142;ENST00000400215;ENST00000541004	D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48	5.23	5.23	0.72850	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.83972	0.5370	N	0.01235	-0.94	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	D	0.85504	0.1193	9	.	.	.	-23.5277	15.4263	0.75055	0.0:0.0:0.0:1.0	.	159;217	B4E2J1;Q8NBU5	.;ATAD1_HUMAN	L	217;217;159;217	ENSP00000339017:M217L;ENSP00000339016:M217L;ENSP00000412968:M159L;ENSP00000445500:M217L	.	M	-	1	0	ATAD1	89526099	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.673000	0.83973	2.099000	0.63709	0.460000	0.39030	ATG		0.378	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810		13	220	13	220
NPAT	4863	hgsc.bcm.edu;broad.mit.edu	37	11	108043929	108043929	+	Silent	SNP	A	A	G	rs192893789	byFrequency	TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr11:108043929A>G	ENST00000278612.8	-	13	1887	c.1782T>C	c.(1780-1782)aaT>aaC	p.N594N	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	594					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TATCTTGGCAATTTGATAGCT	0.313													A|||	3	0.000599042	0.0	0.0029	5008	,	,		19654	0.0		0.0	False		,,,				2504	0.001															0													123.0	118.0	119.0					11																	108043929		1828	4082	5910	SO:0001819	synonymous_variant	4863			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1782T>C	11.37:g.108043929A>G			A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	37	CCDS41710.1																																																																																				0.313	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		9	131	9	131
NCAM1	4684	hgsc.bcm.edu;broad.mit.edu	37	11	113076288	113076288	+	Silent	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr11:113076288G>A	ENST00000533760.1	+	4	635	c.36G>A	c.(34-36)cgG>cgA	p.R12R	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Silent_p.R129R|NCAM1_ENST00000316851.7_Silent_p.R120R	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	130					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGAGTTCCGGGAGGGGGAAG	0.507																																																0													109.0	110.0	109.0					11																	113076288		1986	4143	6129	SO:0001819	synonymous_variant	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.36G>A	11.37:g.113076288G>A			A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Silent	SNP	ENST00000533760.1	37																																																																																					0.507	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		7	100	7	100
KRT76	51350	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	53169301	53169301	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr12:53169301C>T	ENST00000332411.2	-	2	739	c.686G>A	c.(685-687)aGc>aAc	p.S229N		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	229	Linker 1.|Rod.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AGGCTCCAGGCTGCTGGGCCC	0.557																																																0													124.0	127.0	126.0					12																	53169301		2203	4300	6503	SO:0001583	missense	51350			M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.686G>A	12.37:g.53169301C>T	ENSP00000330101:p.Ser229Asn		B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	.	.	.	.	.	.	.	.	.	.	C	0.040	-1.288775	0.01387	.	.	ENSG00000185069	ENST00000332411	T	0.75367	-0.93	4.29	3.05	0.35203	Filament (1);	0.128334	0.35151	N	0.003406	T	0.36220	0.0959	N	0.00754	-1.215	0.30827	N	0.737114	B	0.18741	0.03	B	0.15052	0.012	T	0.43653	-0.9378	10	0.02654	T	1	.	8.4481	0.32854	0.0:0.1117:0.0:0.8882	.	229	Q01546	K22O_HUMAN	N	229	ENSP00000330101:S229N	ENSP00000330101:S229N	S	-	2	0	KRT76	51455568	0.189000	0.23263	0.865000	0.33974	0.284000	0.27059	-0.090000	0.11163	0.670000	0.31165	0.462000	0.41574	AGC		0.557	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848		80	115	80	115
REM2	161253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	23354069	23354069	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr14:23354069C>T	ENST00000267396.4	+	2	413	c.290C>T	c.(289-291)tCg>tTg	p.S97L	REM2_ENST00000536884.1_Missense_Mutation_p.S97L	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	97					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		TCCTCTGGCTCGTCTGACTCC	0.612																																																0													39.0	44.0	42.0					14																	23354069		2177	4277	6454	SO:0001583	missense	161253				CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"""RAS (RAD and GEM) like GTP binding 2"""			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.290C>T	14.37:g.23354069C>T	ENSP00000267396:p.Ser97Leu		B7Z5P1|Q8N8R8	Missense_Mutation	SNP	ENST00000267396.4	37	CCDS45082.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845185	0.71603	.	.	ENSG00000139890	ENST00000267396;ENST00000536884	T;T	0.68765	-0.35;1.24	6.02	6.02	0.97574	.	0.185831	0.48767	D	0.000180	T	0.57695	0.2071	L	0.29908	0.895	0.38903	D	0.957359	D;P	0.55800	0.973;0.635	B;B	0.43018	0.405;0.06	T	0.61491	-0.7052	10	0.41790	T	0.15	.	15.466	0.75400	0.0:0.8609:0.1391:0.0	.	97;97	B7Z5P1;Q8IYK8	.;REM2_HUMAN	L	97	ENSP00000267396:S97L;ENSP00000442774:S97L	ENSP00000267396:S97L	S	+	2	0	REM2	22423909	0.316000	0.24580	0.988000	0.46212	0.749000	0.42624	2.048000	0.41278	2.865000	0.98341	0.655000	0.94253	TCG		0.612	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527		14	94	14	94
CDC42BPB	9578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	103430859	103430859	+	Silent	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr14:103430859G>A	ENST00000361246.2	-	19	2994	c.2706C>T	c.(2704-2706)gaC>gaT	p.D902D		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TGAGGTTGGCGTCCTTGACCT	0.652																																																0													73.0	66.0	69.0					14																	103430859		2203	4300	6503	SO:0001819	synonymous_variant	9578			AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2706C>T	14.37:g.103430859G>A				Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																				0.652	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		16	63	16	63
NDN	4692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	23932264	23932264	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr15:23932264G>A	ENST00000331837.4	-	1	186	c.101C>T	c.(100-102)cCg>cTg	p.P34L		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	34					axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GGTCGCGGACGGAGGAACCCC	0.692									Prader-Willi syndrome																																							0													12.0	12.0	12.0					15																	23932264		1715	3435	5150	SO:0001583	missense	4692	Familial Cancer Database	Prader-Labhart-Willi syndrome	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"""Prader-Willi syndrome chromosome region"""	602117	"""necdin (mouse) homolog"", ""necdin homolog (mouse)"""			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.101C>T	15.37:g.23932264G>A	ENSP00000332643:p.Pro34Leu		B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	37	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.891073	0.33348	.	.	ENSG00000182636	ENST00000331837	T	0.02323	4.34	3.09	2.17	0.27698	.	1.110270	0.06821	N	0.792319	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43893	-0.9363	10	0.52906	T	0.07	.	5.9999	0.19515	0.1427:0.0:0.8573:0.0	.	34	Q99608	NECD_HUMAN	L	34	ENSP00000332643:P34L	ENSP00000332643:P34L	P	-	2	0	NDN	21483357	0.345000	0.24835	0.001000	0.08648	0.012000	0.07955	0.702000	0.25631	0.865000	0.35603	0.561000	0.74099	CCG		0.692	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		7	27	7	27
ITGA11	22801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	68643096	68643096	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr15:68643096C>T	ENST00000315757.7	-	9	1005	c.919G>A	c.(919-921)Ggg>Agg	p.G307R	ITGA11_ENST00000423218.2_Missense_Mutation_p.G307R|ITGA11_ENST00000562826.1_5'Flank	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	307	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GGATTGATCCCCCTGCGGTTG	0.502																																																0													83.0	87.0	86.0					15																	68643096		1884	4105	5989	SO:0001583	missense	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.919G>A	15.37:g.68643096C>T	ENSP00000327290:p.Gly307Arg		J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319235	0.81469	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.53857	0.6;0.6	5.19	5.19	0.71726	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.70613	0.3244	M	0.62723	1.935	0.58432	D	0.999993	D;D	0.89917	0.998;1.0	D;D	0.97110	0.985;1.0	T	0.71374	-0.4612	10	0.49607	T	0.09	.	17.6983	0.88288	0.0:1.0:0.0:0.0	.	307;307	A8K8T0;Q9UKX5	.;ITA11_HUMAN	R	307	ENSP00000327290:G307R;ENSP00000403392:G307R	ENSP00000327290:G307R	G	-	1	0	ITGA11	66430150	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.872000	0.56085	2.403000	0.81681	0.549000	0.68633	GGG		0.502	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		29	86	29	86
ATXN2L	11273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	28846974	28846974	+	Silent	SNP	T	T	C			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr16:28846974T>C	ENST00000336783.4	+	21	2957	c.2790T>C	c.(2788-2790)ccT>ccC	p.P930P	ATXN2L_ENST00000340394.8_Silent_p.P930P|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000325215.6_Silent_p.P930P|ATXN2L_ENST00000382686.4_Silent_p.P930P|ATXN2L_ENST00000570200.1_Silent_p.P930P|ATXN2L_ENST00000395547.2_Silent_p.P930P|ATXN2L_ENST00000564304.1_Silent_p.P936P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	930					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						CACCGGGACCTTCTGCCCAGT	0.662																																																0													47.0	45.0	45.0					16																	28846974		2197	4300	6497	SO:0001819	synonymous_variant	11273				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2790T>C	16.37:g.28846974T>C			A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Silent	SNP	ENST00000336783.4	37	CCDS10641.1																																																																																				0.662	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		9	72	9	72
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577568	7577568	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr17:7577568C>T	ENST00000269305.4	-	7	902	c.713G>A	c.(712-714)tGt>tAt	p.C238Y	TP53_ENST00000413465.2_Missense_Mutation_p.C238Y|TP53_ENST00000359597.4_Missense_Mutation_p.C238Y|TP53_ENST00000420246.2_Missense_Mutation_p.C238Y|TP53_ENST00000445888.2_Missense_Mutation_p.C238Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C238Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	238	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C238Y(65)|p.C238F(46)|p.C238S(9)|p.0?(8)|p.?(5)|p.C145F(5)|p.C145Y(5)|p.M237_N239delMCN(4)|p.C238fs*21(1)|p.M237fs*1(1)|p.M144_N146delMCN(1)|p.C238del(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.H233fs*6(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.N239_C242del(1)|p.C145S(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAACTGTTACACATGTAGTT	0.572		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	158	Substitution - Missense(131)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(4)	breast(22)|ovary(17)|large_intestine(14)|haematopoietic_and_lymphoid_tissue(13)|endometrium(13)|lung(12)|upper_aerodigestive_tract(9)|pancreas(8)|soft_tissue(7)|urinary_tract(7)|oesophagus(7)|biliary_tract(6)|central_nervous_system(6)|liver(5)|bone(5)|stomach(4)|skin(2)|meninges(1)	GRCh37	CM034930	TP53	M							132.0	103.0	113.0					17																	7577568		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.713G>A	17.37:g.7577568C>T	ENSP00000269305:p.Cys238Tyr		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327056	0.81690	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99964	-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96;-9.96	4.09	4.09	0.47781	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99972	0.9991	M	0.92970	3.365	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.95847	0.8871	10	0.87932	D	0	-18.536	14.6088	0.68501	0.0:1.0:0.0:0.0	.	238;238;145;238;238;238	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Y	238;238;238;238;238;238;227;145;106;145	ENSP00000410739:C238Y;ENSP00000352610:C238Y;ENSP00000269305:C238Y;ENSP00000398846:C238Y;ENSP00000391127:C238Y;ENSP00000391478:C238Y;ENSP00000425104:C106Y;ENSP00000423862:C145Y	ENSP00000269305:C238Y	C	-	2	0	TP53	7518293	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.556000	0.82233	2.564000	0.86499	0.462000	0.41574	TGT		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		46	76	46	76
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578263	7578263	+	Nonsense_Mutation	SNP	G	G	A	rs397516435		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr17:7578263G>A	ENST00000269305.4	-	6	775	c.586C>T	c.(586-588)Cga>Tga	p.R196*	TP53_ENST00000413465.2_Nonsense_Mutation_p.R196*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R196*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R196*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R196*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.R196*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	196	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R196*(167)|p.R64*(14)|p.R103*(14)|p.0?(8)|p.R196fs*51(7)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.R196R(2)|p.I195fs*50(1)|p.R64fs*>27(1)|p.R103fs*51(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I195fs*12(1)|p.P59_E66>Q(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCTTCCACTCGGATAAGATGC	0.552		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	232	Substitution - Nonsense(195)|Deletion - Frameshift(11)|Whole gene deletion(8)|Deletion - In frame(5)|Complex - deletion inframe(5)|Unknown(5)|Substitution - coding silent(2)|Complex - frameshift(1)	large_intestine(54)|breast(29)|upper_aerodigestive_tract(22)|lung(22)|haematopoietic_and_lymphoid_tissue(17)|skin(17)|biliary_tract(11)|central_nervous_system(11)|oesophagus(11)|ovary(11)|stomach(8)|urinary_tract(7)|bone(4)|liver(3)|pancreas(3)|eye(1)|kidney(1)	GRCh37	CM941329	TP53	M							102.0	91.0	94.0					17																	7578263		2203	4300	6503	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.586C>T	17.37:g.7578263G>A	ENSP00000269305:p.Arg196*		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409843	0.42715	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	4.44	0.53790	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.9531	12.3046	0.54895	0.0827:0.0:0.9173:0.0	.	.	.	.	X	196;196;196;196;196;196;185;103;64;103;64	.	ENSP00000269305:R196X	R	-	1	2	TP53	7518988	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	2.166000	0.42406	1.427000	0.47276	-0.140000	0.14226	CGA		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		27	35	27	35
MUC16	94025	hgsc.bcm.edu;broad.mit.edu	37	19	9086351	9086351	+	Missense_Mutation	SNP	T	T	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr19:9086351T>A	ENST00000397910.4	-	1	5667	c.5464A>T	c.(5464-5466)Act>Tct	p.T1822S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1822	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTGATGGAGTTGGAGATGGA	0.483																																																0													176.0	169.0	172.0					19																	9086351		1938	4147	6085	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5464A>T	19.37:g.9086351T>A	ENSP00000381008:p.Thr1822Ser		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	7.031	0.560657	0.13498	.	.	ENSG00000181143	ENST00000397910	T	0.02369	4.32	0.513	-1.03	0.10102	.	.	.	.	.	T	0.03095	0.0091	N	0.08118	0	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.44467	-0.9326	7	0.87932	D	0	.	.	.	.	.	1822	B5ME49	.	S	1822	ENSP00000381008:T1822S	ENSP00000381008:T1822S	T	-	1	0	MUC16	8947351	0.000000	0.05858	0.050000	0.19076	0.684000	0.39900	-1.546000	0.02188	-0.598000	0.05806	0.254000	0.18369	ACT		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		8	137	8	137
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu	37	19	11098500	11098500	+	Missense_Mutation	SNP	G	G	A	rs371214327		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr19:11098500G>A	ENST00000429416.3	+	7	1299	c.1018G>A	c.(1018-1020)Gcg>Acg	p.A340T	SMARCA4_ENST00000358026.2_Missense_Mutation_p.A340T|SMARCA4_ENST00000541122.2_Missense_Mutation_p.A340T|SMARCA4_ENST00000344626.4_Missense_Mutation_p.A340T|SMARCA4_ENST00000444061.3_Missense_Mutation_p.A340T|SMARCA4_ENST00000590574.1_Missense_Mutation_p.A340T|SMARCA4_ENST00000413806.3_Missense_Mutation_p.A340T|SMARCA4_ENST00000589677.1_Missense_Mutation_p.A340T|SMARCA4_ENST00000450717.3_Missense_Mutation_p.A340T	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	340					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGCCCAGCCCGCGCCCATGGT	0.746			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1,4273		0,1,2136	9.0	13.0	12.0		1018,1018,1018,1018,1018,1018,1018	4.4	0.7	19		12	0,8316		0,0,4158	no	missense,missense,missense,missense,missense,missense,missense	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	58,58,58,58,58,58,58	0,1,6294	AA,AG,GG		0.0,0.0234,0.0079	benign,benign,benign,benign,benign,benign,benign	340/1648,340/1618,340/1617,340/1615,340/1614,340/1680,340/1648	11098500	1,12589	2137	4158	6295	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1018G>A	19.37:g.11098500G>A	ENSP00000395654:p.Ala340Thr		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	9.744	1.165626	0.21538	2.34E-4	0.0	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1	4.36	4.36	0.52297	.	0.202096	0.41823	D	0.000816	T	0.72740	0.3498	N	0.12746	0.255	0.21861	N	0.9995	B;B;B;B;B;B;B	0.23806	0.01;0.091;0.007;0.024;0.002;0.051;0.051	B;B;B;B;B;B;B	0.14578	0.006;0.006;0.006;0.011;0.006;0.004;0.004	T	0.55636	-0.8110	10	0.13108	T	0.6	-26.467	11.8129	0.52194	0.0:0.1778:0.8222:0.0	.	340;340;340;340;340;340;340	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	T	340	ENSP00000395654:A340T;ENSP00000350720:A340T;ENSP00000343896:A340T;ENSP00000445036:A340T;ENSP00000392837:A340T;ENSP00000397783:A340T;ENSP00000414727:A340T	ENSP00000343896:A340T	A	+	1	0	SMARCA4	10959500	0.178000	0.23122	0.671000	0.29857	0.965000	0.64279	0.612000	0.24283	2.265000	0.75225	0.561000	0.74099	GCG		0.746	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		11	7	11	7
ATP4A	495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	36054521	36054521	+	Splice_Site	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr19:36054521G>A	ENST00000262623.3	-	1	39	c.11C>T	c.(10-12)gCc>gTc	p.A4V		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	4					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CCCACTCACGGCCTTCCCCAT	0.652																																																0													30.0	34.0	33.0					19																	36054521		2203	4300	6503	SO:0001630	splice_region_variant	495				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.12+1C>T	19.37:g.36054521G>A			O00738	Splice_Site	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722556	0.48728	.	.	ENSG00000105675	ENST00000262623	D	0.93076	-3.16	4.12	1.97	0.26223	ATPase, P-type, gastric H+/K+-transporter, N-terminal (1);	678.748000	0.00496	U	0.000145	D	0.86477	0.5942	N	0.08118	0	0.27672	N	0.946726	B	0.02656	0.0	B	0.01281	0.0	T	0.75980	-0.3126	10	0.45353	T	0.12	.	8.0591	0.30623	0.2047:0.0:0.7953:0.0	.	4	P20648	ATP4A_HUMAN	V	4	ENSP00000262623:A4V	ENSP00000262623:A4V	A	-	2	0	ATP4A	40746361	0.180000	0.23148	0.993000	0.49108	0.957000	0.61999	1.236000	0.32683	0.413000	0.25759	0.549000	0.68633	GCC		0.652	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	Missense_Mutation	9	46	9	46
PANK4	55229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	2440330	2440330	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr1:2440330G>A	ENST00000378466.3	-	19	2290	c.2278C>T	c.(2278-2280)Cgg>Tgg	p.R760W	PANK4_ENST00000435556.3_Missense_Mutation_p.R721W	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	760					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CTGAAGAGCCGGCCGCCCAGC	0.622																																																0													22.0	26.0	25.0					1																	2440330		2195	4295	6490	SO:0001583	missense	55229			AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.2278C>T	1.37:g.2440330G>A	ENSP00000367727:p.Arg760Trp		B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494336	0.85069	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.07444	3.19;3.19	5.31	5.31	0.75309	Domain of unknown function DUF89 (1);	0.421129	0.24195	N	0.040674	T	0.11067	0.0270	L	0.41492	1.28	0.34733	D	0.729996	P;P	0.52577	0.954;0.904	B;P	0.46585	0.443;0.521	T	0.07616	-1.0763	10	0.72032	D	0.01	-14.7157	11.7596	0.51894	0.0:0.0:0.7197:0.2803	.	721;760	E9PHT6;Q9NVE7	.;PANK4_HUMAN	W	760;721	ENSP00000367727:R760W;ENSP00000421433:R721W	ENSP00000367727:R760W	R	-	1	2	PANK4	2430190	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.193000	0.72075	2.507000	0.84556	0.561000	0.74099	CGG		0.622	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			19	24	19	24
ZZZ3	26009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78041829	78041829	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr1:78041829G>A	ENST00000370801.3	-	12	2730	c.2255C>T	c.(2254-2256)cCg>cTg	p.P752L	ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Missense_Mutation_p.P258L	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	752					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						ATACACTGGCGGTTCATGTGA	0.378																																																0													180.0	165.0	170.0					1																	78041829		2203	4300	6503	SO:0001583	missense	26009			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.2255C>T	1.37:g.78041829G>A	ENSP00000359837:p.Pro752Leu		B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	37	CCDS677.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914848	0.92178	.	.	ENSG00000036549	ENST00000370801;ENST00000370798	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.74831	0.3768	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	0.989;1.0;0.99	P;D;P	0.72982	0.579;0.979;0.82	T	0.76621	-0.2892	9	0.72032	D	0.01	.	19.4334	0.94781	0.0:0.0:1.0:0.0	.	258;752;751	Q8IYH5-3;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	L	752;258	.	ENSP00000359834:P258L	P	-	2	0	ZZZ3	77814417	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.185000	0.94900	2.649000	0.89929	0.655000	0.94253	CCG		0.378	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		39	68	39	68
RBMXL1	494115	hgsc.bcm.edu;broad.mit.edu	37	1	89448635	89448635	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr1:89448635C>T	ENST00000321792.5	-	2	1302	c.875G>A	c.(874-876)cGt>cAt	p.R292H	RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.R292H	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	292	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TGGAGCACTACGTGAGTTACC	0.483																																																0													193.0	188.0	190.0					1																	89448635		2203	4300	6503	SO:0001583	missense	494115			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.875G>A	1.37:g.89448635C>T	ENSP00000318415:p.Arg292His			Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.413099	0.25465	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.75477	-0.94;-0.94	1.89	0.911	0.19343	.	0.000000	0.85682	D	0.000000	T	0.39200	0.1069	L	0.39898	1.24	0.33028	D	0.529768	B	0.22851	0.076	B	0.15484	0.013	T	0.03863	-1.0997	10	0.28530	T	0.3	-3.1185	5.9449	0.19213	0.0:0.813:0.0:0.187	.	292	Q96E39	RBMXL_HUMAN	H	292	ENSP00000318415:R292H;ENSP00000446099:R292H	ENSP00000318415:R292H	R	-	2	0	RBMXL1	89221223	1.000000	0.71417	0.995000	0.50966	0.922000	0.55478	3.415000	0.52700	0.129000	0.18514	0.306000	0.20318	CGT		0.483	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		19	301	19	301
ZNF831	128611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	57769660	57769660	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr20:57769660G>A	ENST00000371030.2	+	1	3586	c.3586G>A	c.(3586-3588)Gcg>Acg	p.A1196T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1196							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CCCTCTGCCCGCGGAGCAGAA	0.637																																																0													35.0	40.0	39.0					20																	57769660		2067	4217	6284	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3586G>A	20.37:g.57769660G>A	ENSP00000360069:p.Ala1196Thr		Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	4.688	0.127854	0.08981	.	.	ENSG00000124203	ENST00000371030	T	0.06449	3.3	5.05	-4.52	0.03472	.	1.879040	0.02778	N	0.120554	T	0.04724	0.0128	L	0.33485	1.01	0.09310	N	1	B	0.22541	0.071	B	0.12837	0.008	T	0.33137	-0.9880	10	0.44086	T	0.13	1.2472	1.2848	0.02048	0.226:0.2007:0.3698:0.2035	.	1196	Q5JPB2	ZN831_HUMAN	T	1196	ENSP00000360069:A1196T	ENSP00000360069:A1196T	A	+	1	0	ZNF831	57203055	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.179000	0.09768	-1.354000	0.02188	-2.091000	0.00372	GCG		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		25	24	25	24
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			24	75	24	75
MSX2	4488	hgsc.bcm.edu;broad.mit.edu	37	5	174156254	174156254	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr5:174156254G>A	ENST00000239243.6	+	2	599	c.472G>A	c.(472-474)Gag>Aag	p.E158K	MSX2_ENST00000507785.1_3'UTR	NM_002449.4	NP_002440.2	P35548	MSX2_HUMAN	msh homeobox 2	158					activation of meiosis (GO:0090427)|anagen (GO:0042640)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone trabecula formation (GO:0060346)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte development (GO:0002063)|cranial suture morphogenesis (GO:0060363)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|enamel mineralization (GO:0070166)|endochondral bone growth (GO:0003416)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|frontal suture morphogenesis (GO:0060364)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of catagen (GO:0051795)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of osteoblast differentiation (GO:0045669)|signal transduction involved in regulation of gene expression (GO:0023019)|wound healing, spreading of epidermal cells (GO:0035313)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCTCGCCCTGGAGCGCAAGTT	0.552																																																0													65.0	58.0	61.0					5																	174156254		2203	4300	6503	SO:0001583	missense	4488			D26145	CCDS4392.1	5q35.2	2011-06-20	2006-11-21		ENSG00000120149	ENSG00000120149		"""Homeoboxes / ANTP class : NKL subclass"""	7392	protein-coding gene	gene with protein product	"""craniosynostosis, type 2"""	123101	"""msh (Drosophila) homeo box homolog 2"", ""parietal foramina 1"", ""msh homeobox homolog 2 (Drosophila)"""	PFM1		8668339, 8786091	Standard	XM_006714868		Approved	CRS2, FPP, HOX8, MSH, PFM	uc003mcy.3	P35548	OTTHUMG00000130556	ENST00000239243.6:c.472G>A	5.37:g.174156254G>A	ENSP00000239243:p.Glu158Lys		D3DQN1|Q53XM4|Q9UD60	Missense_Mutation	SNP	ENST00000239243.6	37	CCDS4392.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453551	0.96223	.	.	ENSG00000120149	ENST00000239243	D	0.97575	-4.44	5.72	5.72	0.89469	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98899	0.9627	M	0.92412	3.305	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.99445	1.0939	10	0.87932	D	0	-22.3192	19.8548	0.96752	0.0:0.0:1.0:0.0	.	158	P35548	MSX2_HUMAN	K	158	ENSP00000239243:E158K	ENSP00000239243:E158K	E	+	1	0	MSX2	174088860	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	9.807000	0.99171	2.702000	0.92279	0.591000	0.81541	GAG		0.552	MSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252981.3			4	78	4	78
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	38976646	38976646	+	Missense_Mutation	SNP	A	A	G			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr6:38976646A>G	ENST00000359357.3	+	87	12874	c.12620A>G	c.(12619-12621)aAa>aGa	p.K4207R	DNAH8_ENST00000441566.1_Missense_Mutation_p.K4171R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4207					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATTCAACCCAAAGAGAGTGGA	0.423																																																0													146.0	153.0	150.0					6																	38976646		2203	4300	6503	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12620A>G	6.37:g.38976646A>G	ENSP00000352312:p.Lys4207Arg		O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	33	5.198739	0.94997	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08193	3.12;3.12;3.12	5.68	5.68	0.88126	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.11495	0.0280	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.20840	-1.0263	10	0.10377	T	0.69	.	15.9377	0.79729	1.0:0.0:0.0:0.0	.	4207	Q96JB1	DYH8_HUMAN	R	4412;4207;4171	ENSP00000333363:K4412R;ENSP00000352312:K4207R;ENSP00000402294:K4171R	ENSP00000333363:K4412R	K	+	2	0	DNAH8	39084624	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.159000	0.67721	0.528000	0.53228	AAA		0.423	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		87	158	87	158
PHF10	55274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	170112612	170112612	+	Missense_Mutation	SNP	T	T	C			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr6:170112612T>C	ENST00000339209.4	-	8	950	c.827A>G	c.(826-828)tAt>tGt	p.Y276C	PHF10_ENST00000366780.4_Missense_Mutation_p.Y274C	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	276	SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		TAATGGCAGATACCGCAGCTC	0.438																																																0													122.0	120.0	121.0					6																	170112612		2203	4300	6503	SO:0001583	missense	55274			AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.827A>G	6.37:g.170112612T>C	ENSP00000341805:p.Tyr276Cys		Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	37	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	T	22.1	4.244904	0.79912	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.89810	-2.57;-2.57	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.91700	0.7376	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	0.981;1.0;1.0	P;D;D	0.91635	0.777;0.999;0.964	D	0.92506	0.6012	10	0.59425	D	0.04	-22.5671	14.8138	0.70017	0.0:0.0:0.0:1.0	.	188;274;276	Q5T069;Q8WUB8-2;Q8WUB8	.;.;PHF10_HUMAN	C	274;276	ENSP00000355743:Y274C;ENSP00000341805:Y276C	ENSP00000341805:Y276C	Y	-	2	0	PHF10	169854537	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	7.414000	0.80117	2.160000	0.67779	0.477000	0.44152	TAT		0.438	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		10	117	10	117
TNFSF15	9966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	117552881	117552881	+	Missense_Mutation	SNP	C	C	T	rs150498686		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr9:117552881C>T	ENST00000374045.4	-	4	720	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	TNFSF15_ENST00000374044.1_Missense_Mutation_p.E126K|AL390240.1_ENST00000408807.1_RNA	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	203					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						CTACCTACTTCGCATACAGAC	0.527																																																0								C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	181.0	146.0	158.0		430,607	6.0	1.0	9	dbSNP_134	158	0,8600		0,0,4300	no	missense,missense	TNFSF15	NM_001204344.1,NM_005118.3	56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	144/193,203/252	117552881	1,13005	2203	4300	6503	SO:0001583	missense	9966			AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"""Tumor necrosis factor (ligand) superfamily"""	11931	protein-coding gene	gene with protein product	"""vascular endothelial cell growth inhibitor"", ""TNF superfamily ligand TL1A"", ""TNF ligand-related molecule 1"", ""vascular endothelial growth inhibitor-192A"""	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.607G>A	9.37:g.117552881C>T	ENSP00000363157:p.Glu203Lys		Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974433	0.74246	2.27E-4	0.0	ENSG00000181634	ENST00000374045;ENST00000374044	D;D	0.94417	-3.42;-3.42	6.03	6.03	0.97812	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.131962	0.52532	D	0.000066	D	0.96046	0.8712	L	0.60455	1.87	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.91677	0.5355	10	0.02654	T	1	-32.6912	20.5568	0.99304	0.0:1.0:0.0:0.0	.	203;144	O95150;O95150-2	TNF15_HUMAN;.	K	203;126	ENSP00000363157:E203K;ENSP00000363156:E126K	ENSP00000363156:E126K	E	-	1	0	TNFSF15	116592702	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	4.049000	0.57397	2.861000	0.98227	0.655000	0.94253	GAA		0.527	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118		10	62	10	62
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76939522	76939522	+	Nonsense_Mutation	SNP	A	A	T	rs122445109		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chrX:76939522A>T	ENST00000373344.5	-	9	1440	c.1226T>A	c.(1225-1227)tTg>tAg	p.L409*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.L371*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	409			L -> S (in MRXSHF1). {ECO:0000269|PubMed:15565397}.		ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTCTTCTTCCAATGCAAGATG	0.363			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)	GRCh37	CM056937	ATRX	M	rs122445109						190.0	194.0	193.0					X																	76939522		2203	4296	6499	SO:0001587	stop_gained	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1226T>A	X.37:g.76939522A>T	ENSP00000362441:p.Leu409*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	a	37	6.491045	0.97612	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.06	5.06	0.68205	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-5.2986	13.9857	0.64334	1.0:0.0:0.0:0.0	.	.	.	.	X	409;371;365	.	ENSP00000362441:L409X	L	-	2	0	ATRX	76826178	1.000000	0.71417	0.996000	0.52242	0.692000	0.40212	8.959000	0.93110	1.679000	0.50963	0.414000	0.27820	TTG		0.363	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		241	64	241	64
CCNB1IP1	57820	broad.mit.edu;ucsc.edu	37	14	20779861	20779861	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr14:20779861C>T	ENST00000398169.3	-	7	1298	c.682G>A	c.(682-684)Gat>Aat	p.D228N	CCNB1IP1_ENST00000353689.4_Missense_Mutation_p.D228N|CCNB1IP1_ENST00000437553.2_Missense_Mutation_p.D228N|CCNB1IP1_ENST00000398163.2_Missense_Mutation_p.D228N|CCNB1IP1_ENST00000358932.4_Missense_Mutation_p.D228N|CCNB1IP1_ENST00000398160.2_Missense_Mutation_p.D228N			Q9NPC3	CIP1_HUMAN	cyclin B1 interacting protein 1, E3 ubiquitin protein ligase	228					blastocyst formation (GO:0001825)|chiasma assembly (GO:0051026)|protein ubiquitination (GO:0016567)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D228N(1)	HMGA2/CCNB1IP1(2)	breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	9	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;8.86e-07)|all cancers(55;4.98e-06)	GBM - Glioblastoma multiforme(265;0.0164)		CCATCTCCATCGCCCCGATTT	0.398			T	HMGA2	leiomyoma																																		Dom	yes		14	14q11.2	57820	"""cyclin B1 interacting protein 1, E3 ubiquitin protein ligase"""		M	1	Substitution - Missense(1)	prostate(1)											89.0	91.0	91.0					14																	20779861		2203	4300	6503	SO:0001583	missense	57820			AF216381	CCDS9547.1	14q11.2	2014-02-04	2011-01-31	2004-01-14	ENSG00000100814	ENSG00000100814			19437	protein-coding gene	gene with protein product	"""human enhancer of invasion 10"""	608249	"""chromosome 14 open reading frame 18"", ""cyclin B1 interacting protein 1"""	C14orf18		12612082, 21779533	Standard	NM_021178		Approved	HEI10	uc001vwy.4	Q9NPC3	OTTHUMG00000029509	ENST00000398169.3:c.682G>A	14.37:g.20779861C>T	ENSP00000381235:p.Asp228Asn			Missense_Mutation	SNP	ENST00000398169.3	37	CCDS9547.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125124	0.37533	.	.	ENSG00000100814	ENST00000398160;ENST00000398169;ENST00000358932;ENST00000353689;ENST00000437553;ENST00000398163	.	.	.	5.19	5.19	0.71726	.	0.198103	0.42172	D	0.000744	T	0.22322	0.0538	N	0.08118	0	0.23831	N	0.996726	B	0.02656	0.0	B	0.01281	0.0	T	0.10428	-1.0630	9	0.17832	T	0.49	-9.3444	12.3666	0.55232	0.0:0.8302:0.1698:0.0	.	228	Q9NPC3	CIP1_HUMAN	N	228	.	ENSP00000337396:D228N	D	-	1	0	CCNB1IP1	19849701	0.879000	0.30193	1.000000	0.80357	0.354000	0.29330	2.087000	0.41653	2.573000	0.86826	0.650000	0.86243	GAT		0.398	CCNB1IP1-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073538.3	NM_021178, NM_182849, NM_182851, NM_182852		8	103	8	103
RIOK3	8780	broad.mit.edu;ucsc.edu	37	18	21057190	21057190	+	Missense_Mutation	SNP	C	C	A	rs56187215		TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr18:21057190C>A	ENST00000339486.3	+	11	1919	c.1302C>A	c.(1300-1302)caC>caA	p.H434Q	RIOK3_ENST00000577501.1_Missense_Mutation_p.H434Q|RIOK3_ENST00000581585.1_Missense_Mutation_p.H418Q	NM_003831.3	NP_003822.2	O14730	RIOK3_HUMAN	RIO kinase 3	434	Protein kinase.				chromosome segregation (GO:0007059)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(2)	10	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCCACCCTCACGGCCTGGAGT	0.413																																																0													156.0	138.0	144.0					18																	21057190		2203	4300	6503	SO:0001583	missense	8780			AF013591	CCDS11877.1	18q11.2	2012-12-10	2012-12-10	2003-06-25	ENSG00000101782	ENSG00000101782			11451	protein-coding gene	gene with protein product		603579	"""sudD (suppressor of bimD6, Aspergillus nidulans) homolog"", ""RIO kinase 3 (yeast)"""	SUDD		9602165	Standard	NM_003831		Approved		uc002kui.4	O14730	OTTHUMG00000131813	ENST00000339486.3:c.1302C>A	18.37:g.21057190C>A	ENSP00000341874:p.His434Gln		Q8IXN9	Missense_Mutation	SNP	ENST00000339486.3	37	CCDS11877.1	.	.	.	.	.	.	.	.	.	.	c	14.50	2.553238	0.45487	.	.	ENSG00000101782	ENST00000339486	T	0.06294	3.32	5.96	-7.99	0.01131	RIO kinase (1);Protein kinase-like domain (1);RIO-like kinase (1);	0.096714	0.64402	D	0.000001	T	0.08403	0.0209	L	0.42632	1.34	0.45704	D	0.998611	P;P;P;P	0.45902	0.467;0.788;0.841;0.868	P;P;P;P	0.50970	0.527;0.557;0.524;0.655	T	0.02698	-1.1122	10	0.36615	T	0.2	-15.1387	15.2856	0.73826	0.0:0.5289:0.0:0.4711	.	178;418;434;434	E7ESK5;B4E1Q4;O14730-2;O14730	.;.;.;RIOK3_HUMAN	Q	434	ENSP00000341874:H434Q	ENSP00000341874:H434Q	H	+	3	2	RIOK3	19311188	0.985000	0.35326	0.894000	0.35097	0.960000	0.62799	0.182000	0.16900	-1.247000	0.02507	-0.972000	0.02603	CAC		0.413	RIOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254756.1	NM_003831		53	70	53	70
HSP90AB2P	391634	broad.mit.edu;ucsc.edu	37	4	13339305	13339305	+	RNA	SNP	A	A	T			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr4:13339305A>T	ENST00000602906.1	+	0	862							Q58FF8	H90B2_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 2, pseudogene						protein folding (GO:0006457)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			kidney(3)|lung(1)	4						AAAATCTTCAAAGTCATTCAC	0.423																																																0																																												391634			AY956763		4p15.33	2012-04-18	2011-04-15		ENSG00000205940	ENSG00000205940			32537	pseudogene	pseudogene			"""heat shock protein 90kDa alpha (cytosolic), class B member 2 (pseudogene)"""			16269234	Standard	NG_032979		Approved	HSP90BB		Q58FF8			4.37:g.13339305A>T				RNA	SNP	ENST00000602906.1	37																																																																																					0.423	HSP90AB2P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000359156.2			6	21	6	21
MYH2	4620	broad.mit.edu;ucsc.edu	37	17	10451106	10451106	+	Missense_Mutation	SNP	T	T	A			TCGA-FG-6690-01A-11D-1893-08	TCGA-FG-6690-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68080470-9502-41cb-b0e1-786f2c3fe62a	b8e3eb49-7c11-4317-93ef-7dae88807e25	g.chr17:10451106T>A	ENST00000245503.5	-	3	516	c.132A>T	c.(130-132)aaA>aaT	p.K44N	MYH2_ENST00000397183.2_Missense_Mutation_p.K44N|MYH2_ENST00000532183.2_Missense_Mutation_p.K44N|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	44					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CAAAGGATTCTTTGGGCTCCG	0.537																																																0													126.0	120.0	122.0					17																	10451106		2203	4300	6503	SO:0001583	missense	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.132A>T	17.37:g.10451106T>A	ENSP00000245503:p.Lys44Asn		A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.879490	0.51801	.	.	ENSG00000125414	ENST00000532288;ENST00000532183;ENST00000245503;ENST00000397183;ENST00000420805;ENST00000431502	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	5.67	1.39	0.22231	Myosin, N-terminal, SH3-like (1);	0.000000	0.40908	U	0.000998	D	0.89347	0.6689	M	0.85299	2.745	0.45087	D	0.998106	B;P	0.38745	0.384;0.645	B;P	0.56127	0.377;0.792	D	0.88269	0.2928	10	0.62326	D	0.03	.	10.4342	0.44426	0.0:0.652:0.0:0.348	.	44;44	Q567P6;Q9UKX2	.;MYH2_HUMAN	N	44	ENSP00000433944:K44N;ENSP00000245503:K44N;ENSP00000380367:K44N;ENSP00000399348:K44N;ENSP00000416072:K44N	ENSP00000245503:K44N	K	-	3	2	MYH2	10391831	0.000000	0.05858	1.000000	0.80357	0.970000	0.65996	-2.677000	0.00839	0.323000	0.23307	-0.248000	0.11899	AAA		0.537	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		83	122	83	122
