#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
CFAP43	80217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	105990414	105990414	+	Missense_Mutation	SNP	G	G	A	rs376788209		TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr10:105990414G>A	ENST00000278064.2	-	2	368	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	WDR96_ENST00000428666.1_Missense_Mutation_p.R85W|WDR96_ENST00000369719.1_Missense_Mutation_p.R15W|WDR96_ENST00000357060.3_Missense_Mutation_p.R85W|WDR96_ENST00000369720.1_Missense_Mutation_p.R15W																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TTTAGCTTCCGGTCAGAAAAA	0.423																																																0								G	TRP/ARG	0,4406		0,0,2203	122.0	112.0	116.0		253	4.9	1.0	10		116	1,8599	1.2+/-3.3	0,1,4299	no	missense	WDR96	NM_025145.5	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	85/1666	105990414	1,13005	2203	4300	6503	SO:0001583	missense	80217																														ENST00000278064.2:c.43C>T	10.37:g.105990414G>A	ENSP00000278064:p.Arg15Trp			Missense_Mutation	SNP	ENST00000278064.2	37		.	.	.	.	.	.	.	.	.	.	G	25.2	4.614060	0.87359	0.0	1.16E-4	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720;ENST00000369719	T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43	4.94	4.94	0.65067	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.32785	N	0.005656	T	0.42607	0.1210	M	0.65975	2.015	0.42578	D	0.993203	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.985;0.999;0.985	T	0.40739	-0.9547	10	0.72032	D	0.01	.	18.1677	0.89733	0.0:0.0:1.0:0.0	.	85;85;85	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	W	85;85;15;15;15	ENSP00000349568:R85W;ENSP00000400289:R85W;ENSP00000278064:R15W;ENSP00000358734:R15W;ENSP00000358733:R15W	ENSP00000278064:R15W	R	-	1	2	WDR96	105980404	1.000000	0.71417	0.956000	0.39512	0.922000	0.55478	3.421000	0.52742	2.289000	0.77006	0.484000	0.47621	CGG		0.423	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			56	71	56	71
OR4A16	81327	hgsc.bcm.edu;broad.mit.edu	37	11	55111136	55111136	+	Missense_Mutation	SNP	T	T	G			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr11:55111136T>G	ENST00000314721.2	+	1	510	c.460T>G	c.(460-462)Tct>Gct	p.S154A		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						TTTTGTGCACTCTGTGGTTCA	0.453																																																0													193.0	173.0	180.0					11																	55111136		2201	4296	6497	SO:0001583	missense	81327			AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"""GPCR / Class A : Olfactory receptors"""	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.460T>G	11.37:g.55111136T>G	ENSP00000325128:p.Ser154Ala		Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	t	0.109	-1.141534	0.01728	.	.	ENSG00000181961	ENST00000314721	T	0.38560	1.13	2.69	0.0923	0.14472	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.23766	0.0575	N	0.16266	0.395	0.09310	N	1	B	0.14012	0.009	B	0.30943	0.122	T	0.33523	-0.9865	9	0.22109	T	0.4	.	3.1823	0.06588	0.4:0.0:0.2237:0.3763	.	154	Q8NH70	O4A16_HUMAN	A	154	ENSP00000325128:S154A	ENSP00000325128:S154A	S	+	1	0	OR4A16	54867712	0.000000	0.05858	0.003000	0.11579	0.043000	0.13939	-0.117000	0.10708	-0.103000	0.12175	0.346000	0.21813	TCT		0.453	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		11	171	11	171
NLRX1	79671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	119050958	119050958	+	Missense_Mutation	SNP	G	G	A	rs151306288	byFrequency	TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr11:119050958G>A	ENST00000409109.1	+	7	2815	c.2228G>A	c.(2227-2229)cGc>cAc	p.R743H	NLRX1_ENST00000525863.1_Missense_Mutation_p.R743H|NLRX1_ENST00000292199.2_Missense_Mutation_p.R743H|NLRX1_ENST00000409991.1_Missense_Mutation_p.R743H|NLRX1_ENST00000409265.4_Missense_Mutation_p.R743H	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	743	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GCTGGGCTGCGCACACTCCTG	0.612													G|||	5	0.000998403	0.0023	0.0	5008	,	,		19473	0.0		0.0	False		,,,				2504	0.002															0													35.0	33.0	34.0					11																	119050958		2199	4288	6487	SO:0001583	missense	79671			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2228G>A	11.37:g.119050958G>A	ENSP00000387334:p.Arg743His		A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	G	6.471	0.455007	0.12283	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.17	2.17	0.27698	.	0.269729	0.34338	N	0.004047	T	0.23886	0.0578	N	0.11560	0.145	0.28244	N	0.925545	B;B	0.22983	0.078;0.005	B;B	0.18871	0.023;0.001	T	0.17653	-1.0362	10	0.17369	T	0.5	.	9.3735	0.38268	0.2439:0.0:0.7561:0.0	.	743;743	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	H	743	ENSP00000386851:R743H;ENSP00000292199:R743H;ENSP00000386858:R743H;ENSP00000387334:R743H;ENSP00000433442:R743H	ENSP00000292199:R743H	R	+	2	0	NLRX1	118556168	0.830000	0.29337	0.995000	0.50966	0.102000	0.19082	1.060000	0.30530	0.165000	0.19558	-0.643000	0.03959	CGC		0.612	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		96	53	96	53
CLEC9A	283420	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	10215755	10215755	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr12:10215755T>C	ENST00000355819.1	+	7	1034	c.421T>C	c.(421-423)Tgt>Cgt	p.C141R		NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	141	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						TCAAGAGAATTGTTTAAAGGA	0.368																																																0													119.0	119.0	119.0					12																	10215755		2203	4300	6503	SO:0001583	missense	283420				CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"""C-type lectin domain containing"""	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.421T>C	12.37:g.10215755T>C	ENSP00000348074:p.Cys141Arg		B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	37	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.881611	0.51908	.	.	ENSG00000197992	ENST00000355819	D	0.93547	-3.24	4.52	4.52	0.55395	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.47852	D	0.000210	D	0.97564	0.9202	H	0.96777	3.88	0.54753	D	0.999982	D	0.89917	1.0	D	0.91635	0.999	D	0.97994	1.0356	10	0.87932	D	0	.	10.804	0.46507	0.0:0.0:0.0:1.0	.	141	Q6UXN8	CLC9A_HUMAN	R	141	ENSP00000348074:C141R	ENSP00000348074:C141R	C	+	1	0	CLEC9A	10107022	0.987000	0.35691	0.140000	0.22221	0.032000	0.12392	3.632000	0.54287	1.974000	0.57490	0.482000	0.46254	TGT		0.368	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345		10	114	10	114
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578524	7578524	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr17:7578524G>C	ENST00000269305.4	-	5	595	c.406C>G	c.(406-408)Caa>Gaa	p.Q136E	TP53_ENST00000413465.2_Missense_Mutation_p.Q136E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.Q136E|TP53_ENST00000445888.2_Missense_Mutation_p.Q136E|TP53_ENST00000420246.2_Missense_Mutation_p.Q136E|TP53_ENST00000455263.2_Missense_Mutation_p.Q136E	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	136	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> E (in sporadic cancers; somatic mutation).|Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q136*(34)|p.0?(8)|p.C135fs*9(3)|p.Q136E(3)|p.N131fs*27(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.Q136K(1)|p.S127_Q136del10(1)|p.V73fs*9(1)|p.Q43*(1)|p.Y126fs*11(1)|p.Q4*(1)|p.C3fs*9(1)|p.C42fs*9(1)|p.C135_A138delCQLA(1)|p.Q136_K139delQLAK(1)|p.Q136fs*34(1)|p.C135_T140delCQLAKT(1)|p.Q136fs*13(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(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)	TTGGCCAGTTGGCAAAACATC	0.562		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"""	67	Substitution - Nonsense(36)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(5)|Substitution - Missense(4)|Insertion - In frame(2)|Insertion - Frameshift(1)|Complex - deletion inframe(1)	upper_aerodigestive_tract(9)|ovary(9)|urinary_tract(8)|central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(6)|stomach(5)|breast(4)|bone(4)|large_intestine(3)|oesophagus(3)|skin(3)|lung(3)|soft_tissue(1)|endometrium(1)|pancreas(1)	GRCh37	CM971503	TP53	M							52.0	52.0	52.0					17																	7578524		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.406C>G	17.37:g.7578524G>C	ENSP00000269305:p.Gln136Glu		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	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708589	0.89018	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99789	-6.75;-6.75;-6.75;-6.75;-6.75;-6.75;-6.75;-6.75;-6.75	5.48	5.48	0.80851	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	0.99753	0.9901	M	0.85373	2.75	0.80722	D	1	P;D;P;D;D;D;D	0.67145	0.95;0.977;0.572;0.989;0.996;0.981;0.996	P;D;B;P;D;D;D	0.69654	0.794;0.928;0.197;0.888;0.965;0.941;0.909	D	0.97401	0.9996	10	0.87932	D	0	-25.5387	17.2272	0.86973	0.0:0.0:1.0:0.0	.	97;136;136;43;136;136;136	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	E	136;136;136;136;136;136;125;43;4;43;4;136	ENSP00000410739:Q136E;ENSP00000352610:Q136E;ENSP00000269305:Q136E;ENSP00000398846:Q136E;ENSP00000391127:Q136E;ENSP00000391478:Q136E;ENSP00000425104:Q4E;ENSP00000423862:Q43E;ENSP00000424104:Q136E	ENSP00000269305:Q136E	Q	-	1	0	TP53	7519249	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.809000	0.99208	2.733000	0.93635	0.655000	0.94253	CAA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		82	4	82	4
DOCK7	85440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	62995074	62995074	+	Silent	SNP	A	A	G			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr1:62995074A>G	ENST00000340370.5	-	29	3579	c.3562T>C	c.(3562-3564)Tta>Cta	p.L1188L	DOCK7_ENST00000251157.5_Silent_p.L1219L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1219					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTGGAGAGTAAATTGTGTACC	0.408																																																0													114.0	105.0	108.0					1																	62995074		2203	4300	6503	SO:0001819	synonymous_variant	85440				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.3562T>C	1.37:g.62995074A>G			Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	A	9.281	1.048145	0.19827	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.98	3.69	0.42338	.	.	.	.	.	T	0.59514	0.2199	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53746	-0.8395	4	.	.	.	.	9.6634	0.39969	0.7998:0.0:0.2002:0.0	.	.	.	.	S	390	.	.	F	-	2	0	DOCK7	62767662	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	5.291000	0.65667	0.528000	0.28580	0.482000	0.46254	TTT		0.408	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		44	71	44	71
CFAP45	25790	hgsc.bcm.edu;broad.mit.edu	37	1	159842834	159842834	+	Missense_Mutation	SNP	G	G	A	rs148876212	byFrequency	TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr1:159842834G>A	ENST00000368099.4	-	11	1541	c.1477C>T	c.(1477-1479)Cgg>Tgg	p.R493W	RP11-190A12.7_ENST00000544342.1_5'Flank|CCDC19_ENST00000426543.2_Missense_Mutation_p.R408W|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			GTGGCAATCCGGTTCTGCACT	0.597																																																0								G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	83.0	79.0	81.0		1477	5.3	1.0	1	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CCDC19	NM_012337.2	101	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	probably-damaging	493/552	159842834	4,13002	2203	4300	6503	SO:0001583	missense	25790																														ENST00000368099.4:c.1477C>T	1.37:g.159842834G>A	ENSP00000357079:p.Arg493Trp			Missense_Mutation	SNP	ENST00000368099.4	37	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994216	0.93167	6.81E-4	1.16E-4	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.12569	2.67;2.67	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.34832	0.0911	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.14727	-1.0462	9	.	.	.	-24.1753	16.7323	0.85438	0.0:0.0:1.0:0.0	.	493	Q9UL16	CCD19_HUMAN	W	493;408	ENSP00000357079:R493W;ENSP00000403044:R408W	.	R	-	1	2	CCDC19	158109458	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	4.024000	0.57218	2.609000	0.88269	0.655000	0.94253	CGG		0.597	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			8	109	8	109
PPFIA4	8497	hgsc.bcm.edu;broad.mit.edu	37	1	203025938	203025938	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr1:203025938C>G	ENST00000447715.2	+	24	2642	c.2201C>G	c.(2200-2202)cCc>cGc	p.P734R	PPFIA4_ENST00000414050.2_Missense_Mutation_p.P463R|PPFIA4_ENST00000367240.2_Missense_Mutation_p.P735R|PPFIA4_ENST00000272198.6_Missense_Mutation_p.P250R|PPFIA4_ENST00000599966.1_Missense_Mutation_p.P250R|PPFIA4_ENST00000295706.4_Missense_Mutation_p.P250R			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	734					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GGCAGCAACCCCAGCAGCAGC	0.562																																																0													23.0	27.0	26.0					1																	203025938		2173	4287	6460	SO:0001583	missense	8497			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2201C>G	1.37:g.203025938C>G	ENSP00000402576:p.Pro734Arg		A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	c	17.91	3.503512	0.64298	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.06	5.06	0.68205	.	0.000000	0.45126	D	0.000387	T	0.47691	0.1459	L	0.58810	1.83	0.47511	D	0.999445	B;B;B;B	0.17667	0.023;0.019;0.007;0.004	B;B;B;B	0.23419	0.046;0.032;0.029;0.013	T	0.38845	-0.9642	10	0.21540	T	0.41	-31.0856	18.6163	0.91304	0.0:1.0:0.0:0.0	.	463;734;250;250	B4DIS5;B1N949;O75335-2;O75335	.;.;.;LIPA4_HUMAN	R	735;734;250;463;250	ENSP00000356209:P735R;ENSP00000402576:P734R;ENSP00000295706:P250R;ENSP00000400379:P463R;ENSP00000272198:P250R	ENSP00000272198:P250R	P	+	2	0	PPFIA4	201292561	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.784000	0.38674	2.628000	0.89032	0.556000	0.70494	CCC		0.562	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		4	11	4	11
CHEK2	11200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	29090043	29090043	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr22:29090043C>T	ENST00000405598.1	-	14	1629	c.1438G>A	c.(1438-1440)Gcc>Acc	p.A480T	CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000328354.6_Missense_Mutation_p.A480T|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.A480T|CHEK2_ENST00000402731.1_Missense_Mutation_p.A451T|CHEK2_ENST00000348295.3_Missense_Mutation_p.A451T|CHEK2_ENST00000403642.1_Missense_Mutation_p.A389T|CHEK2_ENST00000544772.1_Missense_Mutation_p.A259T|CHEK2_ENST00000382578.1_Missense_Mutation_p.A389T|CHEK2_ENST00000382580.2_Missense_Mutation_p.A523T|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	480	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						TGTCTTAAGGCTTCTTCTGTC	0.488			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	0													227.0	251.0	242.0					22																	29090043		1389	2350	3739	SO:0001583	missense	11200			AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1438G>A	22.37:g.29090043C>T	ENSP00000386087:p.Ala480Thr		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.003705	0.93287	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382563;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.52983	0.95;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.95	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68007	0.2954	M	0.71920	2.185	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.994;0.992	D;D;D;D;D;P	0.81914	0.991;0.979;0.995;0.989;0.938;0.804	T	0.64605	-0.6368	10	0.32370	T	0.25	-3.8768	18.3006	0.90162	0.0:1.0:0.0:0.0	.	389;259;480;451;480;523	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	T	451;389;163;259;480;480;480;523;389;451	ENSP00000329012:A451T;ENSP00000372021:A389T;ENSP00000442458:A259T;ENSP00000329178:A480T;ENSP00000385747:A480T;ENSP00000386087:A480T;ENSP00000372023:A523T;ENSP00000384919:A389T;ENSP00000384835:A451T	ENSP00000329178:A480T	A	-	1	0	CHEK2	27420043	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.465000	0.66725	2.578000	0.87016	0.555000	0.69702	GCC		0.488	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		115	168	115	168
WDR33	55339	hgsc.bcm.edu;broad.mit.edu	37	2	128477431	128477431	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr2:128477431G>A	ENST00000322313.4	-	16	2326	c.2168C>T	c.(2167-2169)cCt>cTt	p.P723L		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	723	Collagen-like.				mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTGAGGGCCAGGCGGGCCTTG	0.632																																																0													64.0	76.0	72.0					2																	128477431		2203	4300	6503	SO:0001583	missense	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2168C>T	2.37:g.128477431G>A	ENSP00000325377:p.Pro723Leu		Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906772	0.52333	.	.	ENSG00000136709	ENST00000322313	D	0.95554	-3.74	5.37	5.37	0.77165	.	0.075779	0.56097	D	0.000039	D	0.95834	0.8644	M	0.82193	2.58	0.80722	D	1	P	0.42078	0.77	P	0.45449	0.481	D	0.94582	0.7780	10	0.27785	T	0.31	-5.4775	15.0017	0.71476	0.0:0.1421:0.8579:0.0	.	723	Q9C0J8	WDR33_HUMAN	L	723	ENSP00000325377:P723L	ENSP00000325377:P723L	P	-	2	0	WDR33	128193901	1.000000	0.71417	0.994000	0.49952	0.975000	0.68041	3.072000	0.50049	2.676000	0.91093	0.585000	0.79938	CCT		0.632	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		6	95	6	95
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	152383461	152383461	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr2:152383461C>T	ENST00000172853.10	-	120	16960	c.16813G>A	c.(16813-16815)Gcc>Acc	p.A5605T	NEB_ENST00000409198.1_Missense_Mutation_p.A5605T|NEB_ENST00000397345.3_Missense_Mutation_p.A7306T|NEB_ENST00000427231.2_Missense_Mutation_p.A7306T|NEB_ENST00000603639.1_Missense_Mutation_p.A7306T|NEB_ENST00000604864.1_Missense_Mutation_p.A7306T			P20929	NEBU_HUMAN	nebulin	5605					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCCTGAGGGCGAGCACCGTG	0.463																																																0													111.0	115.0	114.0					2																	152383461		1925	4122	6047	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16813G>A	2.37:g.152383461C>T	ENSP00000172853:p.Ala5605Thr		F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	25.0	4.587248	0.86851	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.10477	3.2;3.13;3.11;2.87;3.2	5.98	5.98	0.97165	.	0.098719	0.64402	D	0.000002	T	0.36193	0.0958	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.973;0.992;0.986	T	0.01337	-1.1381	10	0.72032	D	0.01	.	20.4434	0.99119	0.0:1.0:0.0:0.0	.	5605;7306;2036	P20929;F8WCP0;Q14215	NEBU_HUMAN;.;.	T	5605;7306;7306;1654;2036;5605	ENSP00000386259:A5605T;ENSP00000380505:A7306T;ENSP00000416578:A7306T;ENSP00000410961:A2036T;ENSP00000172853:A5605T	ENSP00000172853:A5605T	A	-	1	0	NEB	152091707	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.412000	0.59787	2.838000	0.97847	0.655000	0.94253	GCC		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		7	12	7	12
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	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			44	92	44	92
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	37369109	37369109	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr3:37369109A>G	ENST00000361924.2	+	14	6106	c.5732A>G	c.(5731-5733)cAt>cGt	p.H1911R	GOLGA4_ENST00000356847.4_Missense_Mutation_p.H1933R|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1911	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCCAAATCACATTTGGTCCAA	0.403																																																0													99.0	101.0	100.0					3																	37369109		2203	4300	6503	SO:0001583	missense	2803			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5732A>G	3.37:g.37369109A>G	ENSP00000354486:p.His1911Arg		F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	0.823	-0.748110	0.03065	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.21932	1.99;1.98;1.99	4.08	-3.0	0.05480	.	.	.	.	.	T	0.16214	0.0390	M	0.68317	2.08	0.09310	N	1	B;B;B;B	0.12013	0.005;0.005;0.005;0.001	B;B;B;B	0.09377	0.004;0.004;0.004;0.001	T	0.38134	-0.9675	9	0.18710	T	0.47	.	3.0927	0.06299	0.241:0.1254:0.4523:0.1814	.	1911;1911;1933;1911	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	R	1911;1933;1782	ENSP00000354486:H1911R;ENSP00000349305:H1933R;ENSP00000405842:H1782R	ENSP00000349305:H1933R	H	+	2	0	GOLGA4	37344113	0.000000	0.05858	0.000000	0.03702	0.448000	0.32197	0.334000	0.19787	-0.285000	0.09089	0.448000	0.29417	CAT		0.403	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		56	56	56	56
AMACR	23600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	33989379	33989379	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr5:33989379A>G	ENST00000335606.6	-	5	1056	c.968T>C	c.(967-969)gTg>gCg	p.V323A	AMACR_ENST00000382085.3_Missense_Mutation_p.V323A|AMACR_ENST00000382072.2_3'UTR|AMACR_ENST00000502637.1_Missense_Mutation_p.V308A|AMACR_ENST00000514195.1_5'UTR|RP11-1084J3.4_ENST00000382079.3_3'UTR	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	323					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GCGGGGGCTCACGTCCTGCTC	0.507																																																0													92.0	90.0	91.0					5																	33989379		2203	4300	6503	SO:0001583	missense	23600			AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.968T>C	5.37:g.33989379A>G	ENSP00000334424:p.Val323Ala		A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	A	1.453	-0.564392	0.03939	.	.	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.61980	0.06;0.06;0.06	5.6	3.03	0.35002	CoA-transferase family III domain (1);	0.853418	0.10611	N	0.654465	T	0.47060	0.1425	L	0.35593	1.075	0.18873	N	0.999989	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.30794	-0.9966	10	0.13108	T	0.6	-3.9512	8.4017	0.32590	0.8105:0.0:0.1895:0.0	.	323;308;323	F8W9N1;D6RB81;Q9UHK6	.;.;AMACR_HUMAN	A	323;323;308	ENSP00000334424:V323A;ENSP00000371517:V323A;ENSP00000424351:V308A	ENSP00000334424:V323A	V	-	2	0	AMACR	34025136	0.018000	0.18449	0.108000	0.21378	0.072000	0.16883	2.416000	0.44644	0.401000	0.25424	0.519000	0.50382	GTG		0.507	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		49	100	49	100
OR10C1	442194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	29408070	29408070	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr6:29408070G>A	ENST00000444197.2	+	1	988	c.278G>A	c.(277-279)cGc>cAc	p.R93H	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CACATCTCTCGCTCTGGATGT	0.587																																																0													111.0	107.0	108.0					6																	29408070		1508	2708	4216	SO:0001583	missense	442194				CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.278G>A	6.37:g.29408070G>A	ENSP00000419119:p.Arg93His		Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884573	0.33255	.	.	ENSG00000206474	ENST00000444197	T	0.00397	7.57	3.32	1.49	0.22878	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33591	U	0.004760	T	0.00109	0.0003	N	0.11927	0.2	0.09310	N	1	D	0.69078	0.997	D	0.66602	0.945	T	0.49380	-0.8946	10	0.87932	D	0	.	2.9417	0.05833	0.3922:0.0:0.413:0.1949	.	93	Q96KK4	O10C1_HUMAN	H	93	ENSP00000419119:R93H	ENSP00000419119:R93H	R	+	2	0	OR10C1	29516049	0.000000	0.05858	0.074000	0.20217	0.554000	0.35429	-0.336000	0.07863	0.234000	0.21139	0.196000	0.17591	CGC		0.587	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			57	82	57	82
ZNF425	155054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	148809259	148809259	+	Missense_Mutation	SNP	T	T	A			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr7:148809259T>A	ENST00000378061.2	-	3	406	c.274A>T	c.(274-276)Atg>Ttg	p.M92L	ZNF425_ENST00000484196.1_5'UTR	NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	92					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GTATTCTTCATGTTCAACTGT	0.363																																																0													231.0	205.0	214.0					7																	148809259		2203	4300	6503	SO:0001583	missense	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.274A>T	7.37:g.148809259T>A	ENSP00000367300:p.Met92Leu		B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.713660	0.00706	.	.	ENSG00000204947	ENST00000378061;ENST00000483014	T;T	0.06528	3.29;5.12	3.05	-1.84	0.07809	.	.	.	.	.	T	0.02649	0.0080	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48864	-0.8997	9	0.11182	T	0.66	.	6.7595	0.23532	0.3951:0.0:0.0:0.6049	.	92	Q6IV72	ZN425_HUMAN	L	92;114	ENSP00000367300:M92L;ENSP00000420379:M114L	ENSP00000367300:M92L	M	-	1	0	ZNF425	148440192	0.000000	0.05858	0.005000	0.12908	0.019000	0.09904	0.100000	0.15231	-0.106000	0.12110	-0.347000	0.07816	ATG		0.363	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		18	226	18	226
UNC5D	137970	hgsc.bcm.edu;broad.mit.edu	37	8	35583683	35583683	+	Silent	SNP	C	C	T			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr8:35583683C>T	ENST00000404895.2	+	10	1645	c.1317C>T	c.(1315-1317)ctC>ctT	p.L439L	UNC5D_ENST00000449677.1_Silent_p.L15L|UNC5D_ENST00000416672.1_Silent_p.L444L|UNC5D_ENST00000453357.2_Silent_p.L434L|UNC5D_ENST00000287272.2_Silent_p.L370L|UNC5D_ENST00000420357.1_Silent_p.L372L	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	439					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ACTCCCTGCTCCTGAATTCTG	0.502																																																0													63.0	66.0	65.0					8																	35583683		2203	4300	6503	SO:0001819	synonymous_variant	137970			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1317C>T	8.37:g.35583683C>T			Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																				0.502	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			10	150	10	150
FBXO43	286151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	101146458	101146458	+	Silent	SNP	T	T	C			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr8:101146458T>C	ENST00000428847.2	-	4	2125	c.1809A>G	c.(1807-1809)ggA>ggG	p.G603G		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	603					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.G569V(2)|p.G569G(2)|p.G603G(1)|p.G603V(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			TCAAAACTTCTCCCCAGGGAG	0.408																																																6	Substitution - Missense(3)|Substitution - coding silent(3)	lung(6)											82.0	81.0	81.0					8																	101146458		1845	4089	5934	SO:0001819	synonymous_variant	286151			BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"""F-boxes /  ""other"""""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1809A>G	8.37:g.101146458T>C				Silent	SNP	ENST00000428847.2	37	CCDS47904.1																																																																																				0.408	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		65	70	65	70
LAMC3	10319	hgsc.bcm.edu;broad.mit.edu	37	9	133942444	133942444	+	Silent	SNP	C	C	T	rs145571152	byFrequency	TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr9:133942444C>T	ENST00000361069.4	+	14	2578	c.2445C>T	c.(2443-2445)aaC>aaT	p.N815N	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	815	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GTAGCGGGAACGTGGACCCCA	0.647													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		17172	0.0		0.0	False		,,,				2504	0.0															0								C		10,4396	16.8+/-37.8	0,10,2193	66.0	57.0	60.0		2445	-1.5	0.8	9	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous	LAMC3	NM_006059.3		0,10,6493	TT,TC,CC		0.0,0.227,0.0769		815/1576	133942444	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2445C>T	9.37:g.133942444C>T			B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																				0.647	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		5	43	5	43
ARHGEF1	9138	broad.mit.edu;ucsc.edu	37	19	42396179	42396179	+	Silent	SNP	C	C	T			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr19:42396179C>T	ENST00000354532.3	+	5	457	c.309C>T	c.(307-309)ttC>ttT	p.F103F	ARHGEF1_ENST00000599846.1_Silent_p.F103F|ARHGEF1_ENST00000347545.4_Intron|ARHGEF1_ENST00000337665.4_Silent_p.F118F|ARHGEF1_ENST00000596957.1_3'UTR|ARHGEF1_ENST00000378152.4_Intron	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	103	RGSL.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		ACCACAGCTTCCTGGAGAAGA	0.612																																																0													54.0	51.0	52.0					19																	42396179		2203	4300	6503	SO:0001819	synonymous_variant	9138			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.309C>T	19.37:g.42396179C>T			O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Silent	SNP	ENST00000354532.3	37	CCDS12591.1																																																																																				0.612	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		32	37	32	37
TRPC6	7225	broad.mit.edu;ucsc.edu	37	11	101375482	101375482	+	Missense_Mutation	SNP	C	C	T	rs371919016		TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr11:101375482C>T	ENST00000344327.3	-	2	642	c.218G>A	c.(217-219)cGt>cAt	p.R73H	TRPC6_ENST00000526713.1_5'UTR|TRPC6_ENST00000348423.4_Missense_Mutation_p.R73H|TRPC6_ENST00000360497.4_Missense_Mutation_p.R73H|TRPC6_ENST00000532133.1_Missense_Mutation_p.R73H	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	73					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CCCCTTCTCACGGAGAACTGT	0.463																																					Colon(166;1315 1927 11094 12848 34731)											0													82.0	89.0	86.0					11																	101375482		2203	4299	6502	SO:0001583	missense	7225			AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.218G>A	11.37:g.101375482C>T	ENSP00000340913:p.Arg73His		Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524034	0.85600	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;D	0.81821	-1.34;-1.4;-1.3;-1.54	5.6	5.6	0.85130	.	0.306298	0.35708	N	0.003029	D	0.87613	0.6221	L	0.47190	1.495	0.52501	D	0.999951	D;D;D	0.89917	0.998;1.0;0.997	P;D;P	0.83275	0.891;0.996;0.683	D	0.88200	0.2883	10	0.87932	D	0	-15.021	19.6251	0.95674	0.0:1.0:0.0:0.0	.	73;73;73	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	H	73	ENSP00000340913:R73H;ENSP00000435574:R73H;ENSP00000343672:R73H;ENSP00000353687:R73H	ENSP00000340913:R73H	R	-	2	0	TRPC6	100880692	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.126000	0.71635	2.636000	0.89361	0.655000	0.94253	CGT		0.463	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		76	143	76	143
MTHFD2P1	100287639	broad.mit.edu;ucsc.edu	37	3	95374179	95374179	+	RNA	SNP	C	C	T	rs567358967		TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr3:95374179C>T	ENST00000494840.1	-	0	1682					NR_077228.1				methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1																		GATATTCTAACGGTGGCATCA	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		20384	0.0		0.0	False		,,,				2504	0.001															0																																												100287639					3q11.2	2013-06-19			ENSG00000244681	ENSG00000244681			48859	pseudogene	pseudogene							Standard	NR_077228		Approved				OTTHUMG00000159027		3.37:g.95374179C>T				RNA	SNP	ENST00000494840.1	37																																																																																					0.418	MTHFD2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000352943.1			15	27	15	27
MEGF8	1954	broad.mit.edu;ucsc.edu	37	19	42857651	42857651	+	Silent	SNP	G	G	A			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr19:42857651G>A	ENST00000251268.6	+	21	3585	c.3585G>A	c.(3583-3585)cgG>cgA	p.R1195R	MEGF8_ENST00000334370.4_Silent_p.R1128R	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1195	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				AACGATGCCGGCCCGGCAGCT	0.682																																																0													10.0	11.0	11.0					19																	42857651		2144	4195	6339	SO:0001819	synonymous_variant	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.3585G>A	19.37:g.42857651G>A			A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																					0.682	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		5	31	5	31
MAPK12	6300	broad.mit.edu;ucsc.edu	37	22	50693717	50693717	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr22:50693717G>C	ENST00000215659.8	-	11	1248	c.933C>G	c.(931-933)ttC>ttG	p.F311L	MAPK12_ENST00000497036.1_5'UTR|MAPK12_ENST00000395780.1_Missense_Mutation_p.F221L	NM_002969.3	NP_002960.2	P53778	MK12_HUMAN	mitogen-activated protein kinase 12	311	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle arrest (GO:0007050)|DNA damage induced protein phosphorylation (GO:0006975)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of peptidase activity (GO:0010952)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCAGGGACTCGAAGTAGGGAT	0.612																																																0													123.0	108.0	113.0					22																	50693717		2203	4300	6503	SO:0001583	missense	6300			U66243	CCDS14089.1	22q13.3	2012-05-08			ENSG00000188130	ENSG00000188130	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6874	protein-coding gene	gene with protein product		602399		SAPK3		9169156	Standard	NM_002969		Approved	ERK6, PRKM12, p38gamma, SAPK-3	uc003bkm.1	P53778	OTTHUMG00000030145	ENST00000215659.8:c.933C>G	22.37:g.50693717G>C	ENSP00000215659:p.Phe311Leu		Q14260|Q6IC53|Q99588|Q99672	Missense_Mutation	SNP	ENST00000215659.8	37	CCDS14089.1	.	.	.	.	.	.	.	.	.	.	g	11.22	1.574033	0.28092	.	.	ENSG00000188130	ENST00000438835;ENST00000395780;ENST00000215659	T;T	0.42131	0.98;0.98	4.92	-7.98	0.01135	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.34777	U	0.003693	T	0.41858	0.1177	L	0.35341	1.055	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.972;1.0;1.0;1.0	D;P;D;D;D	0.87578	0.998;0.774;0.997;0.998;0.997	T	0.71803	-0.4482	10	0.02654	T	1	-24.8856	18.8581	0.92262	0.8814:0.0:0.1186:0.0	.	130;73;221;311;301	B7Z274;A8K155;B5MDL5;P53778;F6TXG5	.;.;.;MK12_HUMAN;.	L	301;221;311	ENSP00000379126:F221L;ENSP00000215659:F311L	ENSP00000215659:F311L	F	-	3	2	MAPK12	49035844	0.004000	0.15560	0.710000	0.30468	0.435000	0.31806	-0.678000	0.05209	-1.483000	0.01858	-0.987000	0.02553	TTC		0.612	MAPK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074999.2	NM_002969		63	73	63	73
PDE6C	5146	broad.mit.edu;ucsc.edu	37	10	95385365	95385365	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr10:95385365G>T	ENST00000371447.3	+	5	1036	c.898G>T	c.(898-900)Gaa>Taa	p.E300*		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	300	GAF 2.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.V301_E302del(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	CAAGCTTGGAGAAGTAGAGCC	0.413																																																1	Deletion - In frame(1)	ovary(1)											109.0	96.0	101.0					10																	95385365		2203	4300	6503	SO:0001587	stop_gained	5146			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.898G>T	10.37:g.95385365G>T	ENSP00000360502:p.Glu300*		A6NCR6|Q5VY29	Nonsense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	G	39	7.626320	0.98396	.	.	ENSG00000095464	ENST00000371447	.	.	.	4.69	4.69	0.59074	.	0.097447	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	18.1618	0.89710	0.0:0.0:1.0:0.0	.	.	.	.	X	300	.	ENSP00000360502:E300X	E	+	1	0	PDE6C	95375355	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.601000	0.98297	2.573000	0.86826	0.655000	0.94253	GAA		0.413	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		7	47	7	47
DHX30	22907	broad.mit.edu;hgsc.bcm.edu	37	3	47888021	47888023	+	In_Frame_Del	DEL	ATC	ATC	-			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr3:47888021_47888023delATC	ENST00000445061.1	+	11	1866_1868	c.1459_1461delATC	c.(1459-1461)atcdel	p.I488del	DHX30_ENST00000348968.4_In_Frame_Del_p.I460del|DHX30_ENST00000446256.2_In_Frame_Del_p.I449del|DHX30_ENST00000457607.1_In_Frame_Del_p.I516del	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	488	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CTGCAATGTTATCATCACCCAAC	0.65																																																0																																										SO:0001651	inframe_deletion	22907			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.1459_1461delATC	3.37:g.47888024_47888026delATC	ENSP00000405620:p.Ile488del		A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	In_Frame_Del	DEL	ENST00000445061.1	37	CCDS2759.1																																																																																				0.650	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		64	166	64	166
FSTL5	56884	broad.mit.edu;hgsc.bcm.edu	37	4	162697089	162697089	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr4:162697089delT	ENST00000306100.5	-	5	983	c.547delA	c.(547-549)atgfs	p.M183fs	FSTL5_ENST00000536695.1_Frame_Shift_Del_p.M182fs|FSTL5_ENST00000427802.2_Frame_Shift_Del_p.M182fs|FSTL5_ENST00000379164.4_Frame_Shift_Del_p.M182fs	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	183	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TATTTAAACATTTGATCCACC	0.284																																																0													101.0	103.0	102.0					4																	162697089		2203	4295	6498	SO:0001589	frameshift_variant	56884			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.547delA	4.37:g.162697089delT	ENSP00000305334:p.Met183fs		E9PCP6|Q9NSW7|Q9ULF7	Frame_Shift_Del	DEL	ENST00000306100.5	37	CCDS3802.1																																																																																				0.284	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		47	27	47	27
DHX35	60625	broad.mit.edu;hgsc.bcm.edu	37	20	37591029	37591029	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr20:37591029delC	ENST00000252011.3	+	1	52	c.19delC	c.(19-21)ccgfs	p.P7fs	RP4-616B8.4_ENST00000570096.1_RNA|DHX35_ENST00000373323.4_Frame_Shift_Del_p.P7fs|DHX35_ENST00000373325.2_Frame_Shift_Del_p.P7fs	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	7					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				GCCCGTGGGACCGGTGAAGTT	0.721																																																0													44.0	37.0	39.0					20																	37591029		2202	4300	6502	SO:0001589	frameshift_variant	60625			AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.19delC	20.37:g.37591029delC	ENSP00000252011:p.Pro7fs		A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Frame_Shift_Del	DEL	ENST00000252011.3	37	CCDS13310.1																																																																																				0.721	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		16	14	16	14
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76938271	76938272	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chrX:76938271_76938272delTT	ENST00000373344.5	-	9	2690_2691	c.2476_2477delAA	c.(2476-2478)aagfs	p.K826fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.K788fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	826					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						actcatgctctttatctctttt	0.337			"""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)																																								SO:0001589	frameshift_variant	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.2476_2477delAA	X.37:g.76938271_76938272delTT	ENSP00000362441:p.Lys826fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.337	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		64	13	64	13
NOTCH1	4851	broad.mit.edu	37	9	139393364	139393365	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-DU-7301-01A-11D-2086-08	TCGA-DU-7301-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba94c29b-b76e-4d67-bf5a-ce6bc45d85f8	536cb58b-852c-491a-94f7-ffbea4c98871	g.chr9:139393364_139393365delAT	ENST00000277541.6	-	33	6241_6242	c.6166_6167delAT	c.(6166-6168)atgfs	p.M2056fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2056					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M2057fs*211(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTTGTTCTGCATATCTTTGTTA	0.609			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	1	Deletion - Frameshift(1)	oesophagus(1)																																								SO:0001589	frameshift_variant	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6166_6167delAT	9.37:g.139393366_139393367delAT	ENSP00000277541:p.Met2056fs		Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																				0.609	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		8	313	8	313
