#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
HK1	3098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	71160766	71160766	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr10:71160766C>T	ENST00000359426.6	+	18	2733	c.2629C>T	c.(2629-2631)Cag>Tag	p.Q877*	HK1_ENST00000404387.2_Nonsense_Mutation_p.Q881*|HK1_ENST00000360289.2_Nonsense_Mutation_p.Q865*|HK1_ENST00000298649.3_Nonsense_Mutation_p.Q876*|HK1_ENST00000448642.2_Nonsense_Mutation_p.Q912*	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	877	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AATCATGCACCAGACGGTGAA	0.552																																																0													91.0	84.0	86.0					10																	71160766		2203	4300	6503	SO:0001587	stop_gained	3098			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2629C>T	10.37:g.71160766C>T	ENSP00000352398:p.Gln877*		E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Nonsense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	C	44	10.573930	0.99430	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-17.9209	20.3681	0.98887	0.0:1.0:0.0:0.0	.	.	.	.	X	865;912;881;876;877;877	.	ENSP00000298649:Q876X	Q	+	1	0	HK1	70830772	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.623000	0.61247	2.890000	0.99128	0.655000	0.94253	CAG		0.552	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		23	52	23	52
AMBRA1	55626	hgsc.bcm.edu;broad.mit.edu	37	11	46431879	46431879	+	Silent	SNP	C	C	G			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr11:46431879C>G	ENST00000458649.2	-	16	3574	c.3156G>C	c.(3154-3156)ctG>ctC	p.L1052L	AMBRA1_ENST00000528950.1_Silent_p.L1023L|AMBRA1_ENST00000298834.3_Silent_p.L992L|AMBRA1_ENST00000533727.1_Silent_p.L933L|AMBRA1_ENST00000426438.1_Silent_p.L1023L|AMBRA1_ENST00000534300.1_Silent_p.L992L|AMBRA1_ENST00000314845.3_Silent_p.L962L			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1052					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CCGTCTCGTTCAGCTGGTCCC	0.532																																																0													119.0	104.0	109.0					11																	46431879		2201	4299	6500	SO:0001819	synonymous_variant	55626			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3156G>C	11.37:g.46431879C>G			A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																					0.532	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		7	111	7	111
FNBP4	23360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	47753113	47753113	+	Splice_Site	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr11:47753113C>T	ENST00000263773.5	-	12	1833	c.1821G>A	c.(1819-1821)agG>agA	p.R607R	FNBP4_ENST00000534003.1_5'Flank	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	607	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.					nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						GTCTATGATCCCTAAATTACA	0.438																																																0													89.0	81.0	83.0					11																	47753113		1849	4097	5946	SO:0001630	splice_region_variant	23360			BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1821-1G>A	11.37:g.47753113C>T			Q9H985|Q9NT81|Q9Y2L7	Splice_Site	SNP	ENST00000263773.5	37	CCDS41644.1																																																																																				0.438	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		Silent	24	35	24	35
ARNTL2	56938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	27553705	27553705	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr12:27553705A>T	ENST00000266503.5	+	10	1176	c.1158A>T	c.(1156-1158)caA>caT	p.Q386H	ARNTL2_ENST00000395901.2_Missense_Mutation_p.Q349H|ARNTL2_ENST00000542388.1_Missense_Mutation_p.Q301H|ARNTL2_ENST00000261178.5_Missense_Mutation_p.Q338H|ARNTL2_ENST00000544915.1_Missense_Mutation_p.Q352H|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000311001.5_Missense_Mutation_p.Q372H|ARNTL2_ENST00000546179.1_Missense_Mutation_p.Q349H			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	386	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|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)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					ATGTAGATCAAAGGTAAACAT	0.323																																																0													59.0	63.0	62.0					12																	27553705		2203	4300	6503	SO:0001583	missense	56938			AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.1158A>T	12.37:g.27553705A>T	ENSP00000266503:p.Gln386His		B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.67|17.67	3.447454|3.447454	0.63178|0.63178	.|.	.|.	ENSG00000029153|ENSG00000029153	ENST00000457040|ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388	.|T;T;T;T;T;T;T	.|0.18016	.|2.24;2.24;2.24;2.24;2.24;2.24;2.24	4.05|4.05	0.325|0.325	0.15903|0.15903	.|PAS fold-3 (1);PAS (3);	.|0.201056	.|0.44097	.|D	.|0.000491	T|T	0.27832|0.27832	0.0685|0.0685	L|L	0.46157|0.46157	1.445|1.445	0.58432|0.58432	D|D	0.999993|0.999993	.|D;D;P;P;D;P	.|0.89917	.|0.999;1.0;0.773;0.773;1.0;0.893	.|D;D;P;P;D;P	.|0.79108	.|0.975;0.992;0.586;0.586;0.983;0.903	T|T	0.00756|0.00756	-1.1579|-1.1579	5|10	.|0.40728	.|T	.|0.16	.|.	8.5166|8.5166	0.33250|0.33250	0.4361:0.0:0.5639:0.0|0.4361:0.0:0.5639:0.0	.|.	.|349;352;349;338;372;386	.|F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1	.|.;.;.;.;.;BMAL2_HUMAN	I|H	338|352;349;349;372;338;386;301	.|ENSP00000442438:Q352H;ENSP00000379238:Q349H;ENSP00000438545:Q349H;ENSP00000312247:Q372H;ENSP00000261178:Q338H;ENSP00000266503:Q386H;ENSP00000445836:Q301H	.|ENSP00000261178:Q338H	K|Q	+|+	2|3	0|2	ARNTL2|ARNTL2	27444972|27444972	0.945000|0.945000	0.32115|0.32115	0.992000|0.992000	0.48379|0.48379	0.993000|0.993000	0.82548|0.82548	0.274000|0.274000	0.18680|0.18680	-0.030000|-0.030000	0.13804|0.13804	0.533000|0.533000	0.62120|0.62120	AAA|CAA		0.323	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		21	20	21	20
AKAP13	11214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	86076938	86076938	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr15:86076938T>C	ENST00000394518.2	+	4	400	c.305T>C	c.(304-306)tTc>tCc	p.F102S	AKAP13_ENST00000560302.1_Missense_Mutation_p.F102S|AKAP13_ENST00000361243.2_Missense_Mutation_p.F102S	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	102					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GCAGCTCAATTCCTAGCAACC	0.493																																					Melanoma(94;603 1453 3280 32295 32951)											0													144.0	134.0	137.0					15																	86076938		2202	4299	6501	SO:0001583	missense	11214			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.305T>C	15.37:g.86076938T>C	ENSP00000378026:p.Phe102Ser		Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.424413	0.83667	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.58506	0.33;0.33	5.67	5.67	0.87782	.	.	.	.	.	T	0.70500	0.3231	L	0.46157	1.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.72643	-0.4231	9	0.66056	D	0.02	.	15.3819	0.74664	0.0:0.0:0.0:1.0	.	102;102;102	Q12802;Q12802-2;Q12802-5	AKP13_HUMAN;.;.	S	102;102;101;101	ENSP00000354718:F102S;ENSP00000378026:F102S	ENSP00000354718:F102S	F	+	2	0	AKAP13	83877942	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.461000	0.66699	2.281000	0.76405	0.533000	0.62120	TTC		0.493	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		42	48	42	48
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	A	rs28934576		TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr17:7577120C>A	ENST00000269305.4	-	8	1007	c.818G>T	c.(817-819)cGt>cTt	p.R273L	TP53_ENST00000455263.2_Missense_Mutation_p.R273L|TP53_ENST00000445888.2_Missense_Mutation_p.R273L|TP53_ENST00000420246.2_Missense_Mutation_p.R273L|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.R273L|TP53_ENST00000574684.1_5'Flank	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	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	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"""	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67.0	58.0	61.0					17																	7577120		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.818G>T	17.37:g.7577120C>A	ENSP00000269305:p.Arg273Leu		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	24.6	4.554800	0.86231	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99866	-7.3;-7.3;-7.3;-7.3;-7.3;-7.3	4.92	4.92	0.64577	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	0.99871	0.9939	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.77557	0.988;0.987;0.99;0.986	D	0.96378	0.9279	10	0.87932	D	0	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	L	273;273;273;273;273;262;141	ENSP00000352610:R273L;ENSP00000269305:R273L;ENSP00000398846:R273L;ENSP00000391127:R273L;ENSP00000391478:R273L;ENSP00000425104:R141L	ENSP00000269305:R273L	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		19	7	19	7
MYH4	4622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	10370011	10370011	+	Nonsense_Mutation	SNP	G	G	A	rs373223401		TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr17:10370011G>A	ENST00000255381.2	-	3	162	c.52C>T	c.(52-54)Cga>Tga	p.R18*	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	18					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCAGACTTTCGGAGGAAAGGA	0.478																																																0								G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	107.0	97.0	100.0		52	3.5	1.0	17		100	0,8600		0,0,4300	no	stop-gained	MYH4	NM_017533.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		18/1940	10370011	1,13005	2203	4300	6503	SO:0001587	stop_gained	4622				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.52C>T	17.37:g.10370011G>A	ENSP00000255381:p.Arg18*			Nonsense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430843	0.83776	2.27E-4	0.0	ENSG00000141048	ENST00000255381	.	.	.	4.53	3.48	0.39840	.	0.000000	0.31847	U	0.006970	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.5501	0.68059	0.0:0.0:0.8534:0.1466	.	.	.	.	X	18	.	ENSP00000255381:R18X	R	-	1	2	MYH4	10310736	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.333000	0.43912	2.498000	0.84270	0.650000	0.86243	CGA		0.478	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		16	87	16	87
PIGS	94005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	26890508	26890508	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr17:26890508G>T	ENST00000308360.7	-	5	784	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	PIGS_ENST00000465444.1_5'UTR|PIGS_ENST00000395346.2_Missense_Mutation_p.Q129K|PIGS_ENST00000543734.1_Missense_Mutation_p.Q76K	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	137					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					CCCTCCGCTTGTTCCTGAGGC	0.527																																																0													129.0	103.0	112.0					17																	26890508		2203	4300	6503	SO:0001583	missense	94005				CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.409C>A	17.37:g.26890508G>T	ENSP00000309430:p.Gln137Lys		Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	1.872	-0.460049	0.04508	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.41758	0.99;0.99;0.99	4.93	2.81	0.32909	.	0.513584	0.21682	N	0.070706	T	0.22085	0.0532	L	0.36672	1.1	0.09310	N	1	B;B	0.15719	0.014;0.011	B;B	0.18561	0.022;0.013	T	0.32134	-0.9918	10	0.06099	T	0.92	-9.2285	1.5845	0.02641	0.1606:0.1857:0.4615:0.1921	.	137;129	Q96S52;Q96S52-2	PIGS_HUMAN;.	K	129;137;76	ENSP00000378755:Q129K;ENSP00000309430:Q137K;ENSP00000438447:Q76K	ENSP00000309430:Q137K	Q	-	1	0	PIGS	23914635	0.001000	0.12720	0.156000	0.22583	0.671000	0.39405	0.198000	0.17217	2.437000	0.82529	0.467000	0.42956	CAA		0.527	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		22	37	22	37
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	11095998	11095998	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr19:11095998A>G	ENST00000429416.3	+	4	553	c.272A>G	c.(271-273)aAc>aGc	p.N91S	SMARCA4_ENST00000590574.1_Missense_Mutation_p.N91S|SMARCA4_ENST00000444061.3_Missense_Mutation_p.N91S|SMARCA4_ENST00000541122.2_Missense_Mutation_p.N91S|SMARCA4_ENST00000589677.1_Missense_Mutation_p.N91S|SMARCA4_ENST00000358026.2_Missense_Mutation_p.N91S|SMARCA4_ENST00000413806.3_Missense_Mutation_p.N91S|SMARCA4_ENST00000450717.3_Missense_Mutation_p.N91S|SMARCA4_ENST00000344626.4_Missense_Mutation_p.N91S	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	91	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				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)				CCGCGCTACAACCAGATGAAA	0.632			"""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)											67.0	61.0	63.0					19																	11095998		2203	4300	6503	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.272A>G	19.37:g.11095998A>G	ENSP00000395654:p.Asn91Ser		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.288728	0.23478	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.85556	-2.0;-1.99;-2.0;-1.98;-2.0;-2.0;-1.98	4.78	-2.19	0.07015	.	0.365946	0.29900	N	0.010908	T	0.61311	0.2337	N	0.04508	-0.205	0.21897	N	0.99949	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.0;0.001;0.0	T	0.50750	-0.8791	10	0.16896	T	0.51	-25.9492	7.8438	0.29414	0.4066:0.1313:0.4621:0.0	.	91;91;91;91;91;91;91	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	S	91	ENSP00000395654:N91S;ENSP00000350720:N91S;ENSP00000343896:N91S;ENSP00000445036:N91S;ENSP00000392837:N91S;ENSP00000397783:N91S;ENSP00000414727:N91S	ENSP00000343896:N91S	N	+	2	0	SMARCA4	10956998	0.005000	0.15991	0.896000	0.35187	0.945000	0.59286	0.771000	0.26633	-0.813000	0.04357	-0.250000	0.11733	AAC		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		16	40	16	40
RAVER2	55225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	65268729	65268729	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr1:65268729G>T	ENST00000294428.3	+	6	1254	c.1176G>T	c.(1174-1176)ttG>ttT	p.L392F	RAVER2_ENST00000371072.4_Missense_Mutation_p.L392F|RAVER2_ENST00000430964.2_Missense_Mutation_p.L98F			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	392						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L392F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TTTTACATTTGAATAAAGCAC	0.323																																																1	Substitution - Missense(1)	breast(1)											104.0	99.0	100.0					1																	65268729		1848	4103	5951	SO:0001583	missense	55225			AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.1176G>T	1.37:g.65268729G>T	ENSP00000294428:p.Leu392Phe		Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	37		.	.	.	.	.	.	.	.	.	.	G	7.347	0.622122	0.14193	.	.	ENSG00000162437	ENST00000371072;ENST00000294428;ENST00000430964	T;T	0.47528	0.9;0.84	5.67	2.72	0.32119	.	0.279835	0.34200	N	0.004172	T	0.17109	0.0411	L	0.31752	0.955	0.38976	D	0.958851	B;B	0.24368	0.061;0.102	B;B	0.27380	0.036;0.079	T	0.03910	-1.0993	10	0.29301	T	0.29	-15.093	9.3352	0.38045	0.0746:0.2834:0.642:0.0	.	392;392	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	F	392;392;98	ENSP00000360112:L392F;ENSP00000294428:L392F	ENSP00000294428:L392F	L	+	3	2	RAVER2	65041317	1.000000	0.71417	0.804000	0.32291	0.003000	0.03518	3.148000	0.50647	0.303000	0.22785	-0.179000	0.13096	TTG		0.323	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		11	67	11	67
SLC35D1	23169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	67517761	67517761	+	Splice_Site	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr1:67517761G>A	ENST00000235345.5	-	4	411	c.326C>T	c.(325-327)aCg>aTg	p.T109M	SLC35D1_ENST00000506472.2_Splice_Site_p.T30M	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	109					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						TAGTGGAAACGTCTAGAAAAT	0.299																																																0													64.0	69.0	67.0					1																	67517761		2202	4294	6496	SO:0001630	splice_region_variant	23169			AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"""Solute carriers"""	20800	protein-coding gene	gene with protein product		610804	"""solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"""			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.325-1C>T	1.37:g.67517761G>A			A8K185|B7Z3X2|Q52LU5|Q92548	Splice_Site	SNP	ENST00000235345.5	37	CCDS636.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521092	0.44866	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.64085	-0.08;0.34	5.55	5.55	0.83447	.	0.044496	0.85682	D	0.000000	T	0.38214	0.1032	L	0.31926	0.97	0.58432	D	0.999999	B;B	0.28880	0.226;0.226	B;B	0.17433	0.018;0.011	T	0.26292	-1.0107	10	0.32370	T	0.25	-17.337	18.2671	0.90055	0.0:0.0:1.0:0.0	.	30;109	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	M	109;30	ENSP00000235345:T109M;ENSP00000445189:T30M	ENSP00000235345:T109M	T	-	2	0	SLC35D1	67290349	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.061000	0.57485	2.623000	0.88846	0.585000	0.79938	ACG		0.299	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139	Missense_Mutation	26	38	26	38
UBE2G2	7327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	46207992	46207992	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr21:46207992G>A	ENST00000345496.2	-	2	332	c.62C>T	c.(61-63)cCg>cTg	p.P21L	UBE2G2_ENST00000330942.5_5'UTR|UBE2G2_ENST00000477954.1_5'UTR	NM_003343.5	NP_003334.2	P60604	UB2G2_HUMAN	ubiquitin-conjugating enzyme E2G 2	21					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K48-linked ubiquitination (GO:0070936)|protein N-linked glycosylation via asparagine (GO:0018279)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|central_nervous_system(1)|lung(1)	5				Colorectal(79;0.0638)		AATTCCTTCCGGAGGATTCAG	0.269																																																0													43.0	46.0	45.0					21																	46207992		2201	4300	6501	SO:0001583	missense	7327			BC008351	CCDS13714.1, CCDS33586.1	21q22.3	2011-05-19	2011-05-19		ENSG00000184787	ENSG00000184787		"""Ubiquitin-conjugating enzymes E2"""	12483	protein-coding gene	gene with protein product		603124	"""ubiquitin-conjugating enzyme E2G 2 (homologous to yeast UBC7)"", ""ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast)"""			9693041, 9925943	Standard	NM_003343		Approved	UBC7	uc002zfy.3	P60604	OTTHUMG00000089179	ENST00000345496.2:c.62C>T	21.37:g.46207992G>A	ENSP00000338348:p.Pro21Leu		A6NMQ7|A8K3L4|D3DSL7|P56554	Missense_Mutation	SNP	ENST00000345496.2	37	CCDS13714.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420155	0.83559	.	.	ENSG00000184787	ENST00000345496	T	0.38722	1.12	5.52	5.52	0.82312	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.60805	0.2297	M	0.79693	2.465	0.80722	D	1	D	0.60160	0.987	P	0.55999	0.789	T	0.61964	-0.6954	10	0.39692	T	0.17	-6.8961	16.3909	0.83537	0.0:0.0:1.0:0.0	.	21	P60604	UB2G2_HUMAN	L	21	ENSP00000338348:P21L	ENSP00000338348:P21L	P	-	2	0	UBE2G2	45032420	1.000000	0.71417	0.976000	0.42696	0.915000	0.54546	5.906000	0.69900	2.595000	0.87683	0.655000	0.94253	CCG		0.269	UBE2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202647.2	NM_182688		12	22	12	22
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	21230419	21230419	+	Silent	SNP	G	G	A	rs72653101	byFrequency	TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr2:21230419G>A	ENST00000233242.1	-	26	9448	c.9321C>T	c.(9319-9321)aaC>aaT	p.N3107N		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3107					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAATGTTCTCGTTGTTTCCAG	0.403													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19889	0.001		0.001	False		,,,				2504	0.0															0													102.0	104.0	104.0					2																	21230419		2203	4300	6503	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9321C>T	2.37:g.21230419G>A			O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.403	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			33	47	33	47
WDR54	84058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	74652340	74652340	+	Silent	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr2:74652340G>A	ENST00000348227.4	+	8	862	c.774G>A	c.(772-774)ctG>ctA	p.L258L	WDR54_ENST00000461531.1_3'UTR|WDR54_ENST00000409791.1_Silent_p.L206L	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54	258										breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						TCTGCGCCCTGGACCTGGCTT	0.527																																																0													96.0	95.0	96.0					2																	74652340		2203	4300	6503	SO:0001819	synonymous_variant	84058			AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"""WD repeat domain containing"""	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951	ENST00000348227.4:c.774G>A	2.37:g.74652340G>A			D6W5I3|Q53H85|Q86V45	Silent	SNP	ENST00000348227.4	37	CCDS1940.1																																																																																				0.527	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118		36	70	36	70
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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			10	26	10	26
CCDC149	91050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	24875312	24875312	+	Silent	SNP	T	T	C			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr4:24875312T>C	ENST00000389609.4	-	4	398	c.255A>G	c.(253-255)aaA>aaG	p.K85K	CCDC149_ENST00000502801.1_Silent_p.K85K|CCDC149_ENST00000428116.2_Silent_p.K30K|CCDC149_ENST00000504487.1_Silent_p.K85K	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	30										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				CCTGTTTCCTTTTTTCAGGAG	0.343																																																0													76.0	80.0	78.0					4																	24875312		2203	4300	6503	SO:0001819	synonymous_variant	91050				CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.255A>G	4.37:g.24875312T>C			A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Silent	SNP	ENST00000389609.4	37	CCDS33967.2	.	.	.	.	.	.	.	.	.	.	T	9.298	1.052289	0.19827	.	.	ENSG00000181982	ENST00000382116	.	.	.	5.4	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9322	0.35677	0.0:0.8104:0.0:0.1896	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC149	24484410	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.806000	0.27126	1.325000	0.45301	0.519000	0.50382	.		0.343	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463		8	10	8	10
ADH7	131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	100349018	100349018	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr4:100349018T>A	ENST00000209665.4	-	5	752	c.512A>T	c.(511-513)aAg>aTg	p.K171M	ADH7_ENST00000476959.1_Missense_Mutation_p.K179M|ADH7_ENST00000482593.1_Missense_Mutation_p.K102M|ADH7_ENST00000437033.2_Missense_Mutation_p.K159M	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	171					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		ATCATCAATCTTAGCAACAGA	0.463																																																0													219.0	176.0	191.0					4																	100349018		2203	4300	6503	SO:0001583	missense	131			X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.512A>T	4.37:g.100349018T>A	ENSP00000209665:p.Lys171Met		A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Missense_Mutation	SNP	ENST00000209665.4	37	CCDS34034.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.932349	0.73442	.	.	ENSG00000196344	ENST00000437033;ENST00000209665;ENST00000482593;ENST00000476959;ENST00000474027	T;T;T;T;T	0.04551	3.6;3.6;3.6;3.6;3.6	4.81	3.63	0.41609	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.046452	0.85682	D	0.000000	T	0.28764	0.0713	H	0.95816	3.725	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.20207	-1.0282	10	0.87932	D	0	-21.9699	10.3936	0.44188	0.0:0.077:0.0:0.923	.	171	P40394	ADH7_HUMAN	M	159;171;102;179;102	ENSP00000414254:K159M;ENSP00000209665:K171M;ENSP00000420613:K102M;ENSP00000420269:K179M;ENSP00000420300:K102M	ENSP00000209665:K171M	K	-	2	0	ADH7	100568041	1.000000	0.71417	0.004000	0.12327	0.113000	0.19764	4.351000	0.59398	0.877000	0.35895	0.533000	0.62120	AAG		0.463	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673		8	51	8	51
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	155241554	155241554	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr4:155241554G>A	ENST00000357232.4	-	14	3631	c.3632C>T	c.(3631-3633)aCg>aTg	p.T1211M		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1211	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TAGCATAAACGTCATGTTTTC	0.408																																																0													189.0	167.0	175.0					4																	155241554		2203	4300	6503	SO:0001583	missense	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3632C>T	4.37:g.155241554G>A	ENSP00000349768:p.Thr1211Met		B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	G	2.520	-0.310966	0.05458	.	.	ENSG00000197410	ENST00000357232	T	0.51574	0.7	5.56	2.88	0.33553	Cadherin (4);Cadherin-like (1);	0.831797	0.10808	N	0.631864	T	0.25306	0.0615	N	0.05592	-0.015	0.20703	N	0.999866	B	0.24721	0.11	B	0.20184	0.028	T	0.18745	-1.0327	10	0.44086	T	0.13	.	5.1624	0.15068	0.3043:0.1393:0.5565:0.0	.	1211	Q6V1P9	PCD23_HUMAN	M	1211	ENSP00000349768:T1211M	ENSP00000349768:T1211M	T	-	2	0	DCHS2	155461004	0.411000	0.25384	0.066000	0.19879	0.226000	0.24999	0.950000	0.29122	0.296000	0.22592	0.467000	0.42956	ACG		0.408	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		23	51	23	51
SLC6A18	348932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	1243683	1243683	+	Missense_Mutation	SNP	C	C	T	rs199865996		TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr5:1243683C>T	ENST00000324642.3	+	9	1268	c.1145C>T	c.(1144-1146)cCg>cTg	p.P382L	SLC6A18_ENST00000296821.4_Missense_Mutation_p.P311L	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	382					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GCCTCGGGCCCGGGCCTGGCC	0.647																																																0								C	LEU/PRO	0,4406		0,0,2203	66.0	62.0	64.0		1145	5.0	0.9	5		64	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC6A18	NM_182632.2	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	382/629	1243683	1,13005	2203	4300	6503	SO:0001583	missense	348932			AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1145C>T	5.37:g.1243683C>T	ENSP00000323549:p.Pro382Leu			Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347789	0.61183	0.0	1.16E-4	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.77229	-1.08;-1.08	4.98	4.98	0.66077	.	0.228644	0.37623	N	0.002013	T	0.80513	0.4637	M	0.74389	2.26	0.46609	D	0.999124	D	0.54964	0.969	P	0.44561	0.453	D	0.84835	0.0804	10	0.87932	D	0	.	17.8393	0.88710	0.0:1.0:0.0:0.0	.	382	Q96N87	S6A18_HUMAN	L	382;311	ENSP00000323549:P382L;ENSP00000296821:P311L	ENSP00000296821:P311L	P	+	2	0	SLC6A18	1296683	1.000000	0.71417	0.933000	0.37362	0.164000	0.22412	7.184000	0.77705	2.321000	0.78463	0.561000	0.74099	CCG		0.647	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		9	37	9	37
RNF145	153830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	158601111	158601111	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr5:158601111A>C	ENST00000424310.2	-	6	1036	c.677T>G	c.(676-678)gTa>gGa	p.V226G	RNF145_ENST00000518802.1_Missense_Mutation_p.V256G|RNF145_ENST00000520638.1_Missense_Mutation_p.V240G|RNF145_ENST00000521606.2_Missense_Mutation_p.V243G|RNF145_ENST00000519865.1_Missense_Mutation_p.V226G|RNF145_ENST00000274542.2_Missense_Mutation_p.V254G	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	226						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AACAGGGACTACCAGTTGATT	0.433																																																0													79.0	71.0	74.0					5																	158601111		2203	4300	6503	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.677T>G	5.37:g.158601111A>C	ENSP00000409064:p.Val226Gly		B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499087	0.64298	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.76839	-1.05;-1.04;-1.04;-1.04;-1.04;-1.05;-1.04	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	N	0.08118	0	0.80722	D	1	P;P;P;P;P;P	0.44877	0.81;0.81;0.81;0.81;0.845;0.774	B;B;B;B;B;B	0.43331	0.339;0.339;0.339;0.339;0.416;0.229	T	0.63207	-0.6689	10	0.18710	T	0.47	-12.9464	15.4247	0.75041	1.0:0.0:0.0:0.0	.	242;243;240;256;226;254	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;.;RN145_HUMAN;.	G	254;226;226;242;243;256;226;240	ENSP00000274542:V254G;ENSP00000430397:V226G;ENSP00000409064:V226G;ENSP00000430753:V242G;ENSP00000445115:V243G;ENSP00000430955:V256G;ENSP00000429071:V240G	ENSP00000274542:V254G	V	-	2	0	RNF145	158533689	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	9.287000	0.95975	2.106000	0.64143	0.455000	0.32223	GTA		0.433	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		7	18	7	18
PPP6C	5537	hgsc.bcm.edu;broad.mit.edu	37	9	127933438	127933438	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr9:127933438C>T	ENST00000373547.4	-	2	196	c.97G>A	c.(97-99)Gac>Aac	p.D33N	PPP6C_ENST00000451402.1_Missense_Mutation_p.D70N|PPP6C_ENST00000373546.3_5'UTR|PPP6C_ENST00000415905.1_Missense_Mutation_p.D33N	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit	33					G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						AAGAGGAGGTCACAAACGTAG	0.328																																																0													158.0	150.0	153.0					9																	127933438		2203	4300	6503	SO:0001583	missense	5537			AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.97G>A	9.37:g.127933438C>T	ENSP00000362648:p.Asp33Asn		B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Missense_Mutation	SNP	ENST00000373547.4	37	CCDS6861.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.704634	0.88924	.	.	ENSG00000119414	ENST00000373547;ENST00000451402;ENST00000415905;ENST00000456642	T;T;T;T	0.62788	3.46;3.46;3.46;0.0	5.92	5.92	0.95590	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.000000	0.85682	D	0.000000	T	0.74801	0.3764	M	0.78049	2.395	0.80722	D	1	B;P;B	0.52577	0.38;0.954;0.262	B;P;B	0.51742	0.425;0.678;0.185	T	0.77504	-0.2563	10	0.72032	D	0.01	-30.8606	18.8845	0.92370	0.0:1.0:0.0:0.0	.	33;70;33	O00743-2;O00743-3;O00743	.;.;PPP6_HUMAN	N	33;70;33;21	ENSP00000362648:D33N;ENSP00000392147:D70N;ENSP00000411744:D33N;ENSP00000416287:D21N	ENSP00000362648:D33N	D	-	1	0	PPP6C	126973259	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.882000	0.75589	2.809000	0.96659	0.655000	0.94253	GAC		0.328	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294		33	52	33	52
FAAH2	158584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	57358192	57358192	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chrX:57358192C>T	ENST00000374900.4	+	4	694	c.574C>T	c.(574-576)Cga>Tga	p.R192*		NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	192						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						GATCTATGGCCGATCAAACAA	0.403										HNSCC(52;0.14)																																						0													182.0	142.0	156.0					X																	57358192		2203	4300	6503	SO:0001587	stop_gained	158584			AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"""amidase domain containing"""	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.574C>T	X.37:g.57358192C>T	ENSP00000364035:p.Arg192*		Q86VT2|Q96N98	Nonsense_Mutation	SNP	ENST00000374900.4	37	CCDS14375.1	.	.	.	.	.	.	.	.	.	.	c	13.59	2.282203	0.40394	.	.	ENSG00000165591	ENST00000374900	.	.	.	2.25	-2.01	0.07410	.	0.290091	0.25783	U	0.028337	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.2814	0.10834	0.4896:0.3684:0.0:0.1419	.	.	.	.	X	192	.	ENSP00000364035:R192X	R	+	1	2	FAAH2	57374917	0.895000	0.30542	0.732000	0.30844	0.091000	0.18340	0.425000	0.21346	-0.445000	0.07159	-1.888000	0.00539	CGA		0.403	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		44	13	44	13
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76938920	76938920	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chrX:76938920G>A	ENST00000373344.5	-	9	2042	c.1828C>T	c.(1828-1830)Caa>Taa	p.Q610*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.Q572*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	610					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						TCTTTATCTTGTGGAACTTCC	0.358			"""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)											194.0	219.0	210.0					X																	76938920		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.1828C>T	X.37:g.76938920G>A	ENSP00000362441:p.Gln610*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	g	38	7.234536	0.98154	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.22	5.22	0.72569	.	0.177625	0.42294	D	0.000735	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-3.8042	8.6155	0.33829	0.0:0.2207:0.6378:0.1415	.	.	.	.	X	610;572;537	.	ENSP00000362441:Q610X	Q	-	1	0	ATRX	76825576	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.691000	0.47010	2.177000	0.69029	0.509000	0.49947	CAA		0.358	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		114	43	114	43
KLK15	55554	broad.mit.edu;ucsc.edu	37	19	51330985	51330985	+	Missense_Mutation	SNP	G	G	A	rs140896741	byFrequency	TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr19:51330985G>A	ENST00000598239.1	-	2	160	c.130C>T	c.(130-132)Cgc>Tgc	p.R44C	KLK15_ENST00000596931.1_Missense_Mutation_p.R43C|AC011523.2_ENST00000598079.1_RNA|KLK15_ENST00000416184.1_Missense_Mutation_p.R44C|KLK15_ENST00000301421.2_Missense_Mutation_p.R44C|KLK15_ENST00000326856.4_Missense_Mutation_p.R43C	NM_017509.2	NP_059979.2	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15	44	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		CAGTTAAAGCGTCCACGCTCG	0.612																																					Pancreas(140;10 2513 7143 9246)											0								G	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	98.0	72.0	81.0		130,130,130	3.6	0.0	19	dbSNP_134	81	3,8587	3.0+/-9.4	0,3,4292	yes	missense,missense,missense	KLK15	NM_017509.2,NM_138563.1,NM_138564.1	180,180,180	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging	44/257,44/162,44/172	51330985	3,12993	2203	4295	6498	SO:0001583	missense	55554			AF242195	CCDS12805.1, CCDS12806.1, CCDS12806.2, CCDS62766.1	19q13.4	2008-02-05	2006-10-27			ENSG00000174562		"""Kallikreins"""	20453	protein-coding gene	gene with protein product		610601	"""kallikrein 15"""			11010966, 12439720, 16800724, 16800723	Standard	NM_017509		Approved	HSRNASPH, ACO, prostinogen	uc002ptl.3	Q9H2R5		ENST00000598239.1:c.130C>T	19.37:g.51330985G>A	ENSP00000469315:p.Arg44Cys		A0AUY8|Q15358|Q6ISI0|Q9H2R3|Q9H2R4|Q9H2R6|Q9HBG9	Missense_Mutation	SNP	ENST00000598239.1	37	CCDS12805.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252707	0.59212	0.0	3.49E-4	ENSG00000174562	ENST00000326856;ENST00000416184;ENST00000301421;ENST00000544946	D;D	0.89196	-2.48;-2.48	4.66	3.62	0.41486	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.43416	D	0.000569	D	0.91981	0.7460	M	0.66506	2.035	0.43517	D	0.995781	D;D;B;D	0.89917	0.962;1.0;0.383;1.0	B;D;B;D	0.79784	0.236;0.959;0.167;0.993	D	0.91211	0.4999	10	0.66056	D	0.02	.	7.3009	0.26420	0.1977:0.0:0.8023:0.0	.	44;43;44;44	Q6UBM2;Q6ISI0;Q9H2R5-4;Q9H2R5	.;.;.;KLK15_HUMAN	C	44	ENSP00000415136:R44C;ENSP00000301421:R44C	ENSP00000301421:R44C	R	-	1	0	KLK15	56022797	1.000000	0.71417	0.017000	0.16124	0.815000	0.46073	4.427000	0.59888	1.324000	0.45282	0.561000	0.74099	CGC		0.612	KLK15-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465160.1	NM_017509		17	30	17	30
CSF3	1440	broad.mit.edu;ucsc.edu	37	17	38172560	38172560	+	Silent	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr17:38172560C>T	ENST00000225474.2	+	3	310	c.279C>T	c.(277-279)ccC>ccT	p.P93P	RP11-387H17.6_ENST00000583462.1_lincRNA|CSF3_ENST00000577675.1_Intron|CSF3_ENST00000394148.3_Intron|CSF3_ENST00000394149.3_Silent_p.P90P|CSF3_ENST00000331769.2_Silent_p.P86P			P09919	CSF3_HUMAN	colony stimulating factor 3 (granulocyte)	93					cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|granulocyte differentiation (GO:0030851)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of neuron death (GO:1901215)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|granulocyte colony-stimulating factor receptor binding (GO:0005130)			endometrium(1)|ovary(1)|prostate(1)	3	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)				CCTGGGCTCCCCTGAGCAGCT	0.632																																																0													22.0	20.0	20.0					17																	38172560		2202	4295	6497	SO:0001819	synonymous_variant	1440				CCDS11357.1, CCDS11358.1, CCDS42314.1, CCDS11358.2	17q11.2-q12	2014-01-30			ENSG00000108342	ENSG00000108342		"""Endogenous ligands"""	2438	protein-coding gene	gene with protein product	"""granulocyte colony stimulating factor"", ""pluripoietin"", ""filgrastim"", ""lenograstim"""	138970	"""chromosome 17 open reading frame 33"""	GCSF, G-CSF, C17orf33		3499671, 3501046	Standard	NM_000759		Approved	MGC45931	uc002htp.3	P09919	OTTHUMG00000133247	ENST00000225474.2:c.279C>T	17.37:g.38172560C>T			A8MXR7	Silent	SNP	ENST00000225474.2	37	CCDS11357.1																																																																																				0.632	CSF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256988.2	NM_172220		8	8	8	8
NUP188	23511	broad.mit.edu;ucsc.edu	37	9	131768629	131768629	+	Silent	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr9:131768629G>A	ENST00000372577.2	+	43	5076	c.5055G>A	c.(5053-5055)caG>caA	p.Q1685Q	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1685					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GGATGAAGCAGGAGCTCAGCT	0.592											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													115.0	126.0	122.0					9																	131768629		2203	4300	6503	SO:0001819	synonymous_variant	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.5055G>A	9.37:g.131768629G>A		1590	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																				0.592	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			24	253	24	253
AQP10	89872	broad.mit.edu;ucsc.edu	37	1	154295506	154295506	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr1:154295506G>A	ENST00000324978.3	+	3	321	c.281G>A	c.(280-282)cGc>cAc	p.R94H	AQP10_ENST00000355197.4_3'UTR|ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000484864.1_Missense_Mutation_p.R94H	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	94					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATCGTTGGACGCCTCCCCTGG	0.532																																																0													143.0	133.0	136.0					1																	154295506		2203	4300	6503	SO:0001583	missense	89872			AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"""Ion channels / Aquaporins"""	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.281G>A	1.37:g.154295506G>A	ENSP00000318355:p.Arg94His		Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	37	CCDS1065.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692803	0.48202	.	.	ENSG00000143595	ENST00000324978;ENST00000484864	D;D	0.85702	-2.02;-2.02	5.04	3.17	0.36434	Aquaporin-like (2);	0.056466	0.64402	N	0.000002	T	0.67878	0.2940	L	0.54965	1.715	0.31293	N	0.689225	B;B	0.31383	0.321;0.141	B;B	0.29663	0.105;0.019	T	0.61758	-0.6997	10	0.49607	T	0.09	.	8.6313	0.33922	0.251:0.0:0.749:0.0	.	94;94	Q96PS8-2;Q96PS8	.;AQP10_HUMAN	H	94	ENSP00000318355:R94H;ENSP00000420341:R94H	ENSP00000318355:R94H	R	+	2	0	AQP10	152562130	0.014000	0.17966	0.978000	0.43139	0.956000	0.61745	2.016000	0.40971	0.728000	0.32382	0.555000	0.69702	CGC		0.532	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		10	89	10	89
DAP	1611	broad.mit.edu;ucsc.edu	37	5	10748365	10748365	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A614-01A-11D-A29Q-08	TCGA-HT-A614-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a8c8f66c-25bc-4dea-9ac2-6cafdd75a489	f812a450-4c23-4684-bb9d-b2db9a185156	g.chr5:10748365C>T	ENST00000230895.6	-	2	277	c.74G>A	c.(73-75)cGa>cAa	p.R25Q	DAP_ENST00000432074.2_Missense_Mutation_p.R25Q|DAP_ENST00000510546.1_5'UTR	NM_004394.2	NP_004385.1	P51397	DAP1_HUMAN	death-associated protein	25					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cellular response to amino acid starvation (GO:0034198)|negative regulation of autophagy (GO:0010507)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)		death domain binding (GO:0070513)	p.R25Q(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				CTGCACAATTCGCATTCCACC	0.502																																																1	Substitution - Missense(1)	large_intestine(1)											205.0	164.0	178.0					5																	10748365		2203	4300	6503	SO:0001583	missense	1611			X76105	CCDS3880.1	5p15.2	2008-07-18			ENSG00000112977	ENSG00000112977			2672	protein-coding gene	gene with protein product		600954				8530096, 7828849	Standard	NM_004394		Approved		uc003jez.4	P51397	OTTHUMG00000131041	ENST00000230895.6:c.74G>A	5.37:g.10748365C>T	ENSP00000230895:p.Arg25Gln		Q6FGC3|Q9BUC9	Missense_Mutation	SNP	ENST00000230895.6	37	CCDS3880.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816953	0.70912	.	.	ENSG00000112977	ENST00000230895;ENST00000432074	T;T	0.61859	0.07;0.07	5.04	3.24	0.37175	.	.	.	.	.	T	0.74558	0.3732	M	0.85099	2.735	0.35460	D	0.79644	D;D	0.89917	0.996;1.0	P;D	0.83275	0.643;0.996	T	0.78999	-0.1982	9	0.87932	D	0	.	7.5169	0.27606	0.1635:0.7504:0.0:0.0861	.	25;25	B4DQ75;P51397	.;DAP1_HUMAN	Q	25	ENSP00000230895:R25Q;ENSP00000394163:R25Q	ENSP00000230895:R25Q	R	-	2	0	DAP	10801365	1.000000	0.71417	0.391000	0.26233	0.951000	0.60555	4.581000	0.60949	0.519000	0.28406	0.655000	0.94253	CGA		0.502	DAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253687.1	NM_004394		15	25	15	25
