#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
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	24832988	24832988	+	Nonsense_Mutation	SNP	A	A	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr10:24832988A>T	ENST00000376454.3	+	19	4819	c.4789A>T	c.(4789-4791)Aag>Tag	p.K1597*	KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376451.2_Nonsense_Mutation_p.K1280*|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376462.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1597					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TAAAACAGGGAAGAAGACTTT	0.463																																																0													106.0	107.0	107.0					10																	24832988		2203	4300	6503	SO:0001587	stop_gained	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4789A>T	10.37:g.24832988A>T	ENSP00000365637:p.Lys1597*		A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Nonsense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	43	10.024211	0.99319	.	.	ENSG00000120549	ENST00000442879;ENST00000376454;ENST00000450158;ENST00000376451	.	.	.	5.35	5.35	0.76521	.	0.056516	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3103	0.74026	1.0:0.0:0.0:0.0	.	.	.	.	X	1280;1597;1280;1280	.	ENSP00000365634:K1280X	K	+	1	0	KIAA1217	24872994	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	8.897000	0.92532	2.018000	0.59344	0.459000	0.35465	AAG		0.463	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		13	122	13	122
AGAP5	729092	hgsc.bcm.edu;broad.mit.edu	37	10	75457306	75457306	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr10:75457306G>A	ENST00000374094.4	-	1	248	c.208C>T	c.(208-210)Cag>Tag	p.Q70*	AGAP5_ENST00000443782.2_Nonsense_Mutation_p.Q70*|RP11-464F9.1_ENST00000399449.3_RNA|RP11-574K11.28_ENST00000580790.1_RNA	NM_001144000.1	NP_001137472.1	A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 5	70					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(5)|skin(1)	12						GGCATCTCCTGGTCACGAATG	0.592																																																0													137.0	120.0	125.0					10																	75457306		692	1591	2283	SO:0001587	stop_gained	729092				CCDS44439.1	10q22.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000172650	ENSG00000172650		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23467	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 2"""	CTGLF2			Standard	NM_001144000		Approved	Em:AC073389.1	uc009xri.3	A6NIR3	OTTHUMG00000018473	ENST00000374094.4:c.208C>T	10.37:g.75457306G>A	ENSP00000363207:p.Gln70*		A8MSN5	Nonsense_Mutation	SNP	ENST00000374094.4	37	CCDS44439.1	.	.	.	.	.	.	.	.	.	.	-	16.05	3.013319	0.54468	.	.	ENSG00000172650	ENST00000374094;ENST00000443782	.	.	.	1.4	1.4	0.22301	.	0.119796	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	6.2475	0.20827	0.0:0.0:1.0:0.0	.	.	.	.	X	70	.	ENSP00000363207:Q70X	Q	-	1	0	AGAP5	75127312	1.000000	0.71417	0.997000	0.53966	0.042000	0.13812	0.585000	0.23879	1.094000	0.41399	0.184000	0.17185	CAG		0.592	AGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_001132585		15	197	15	197
HELLS	3070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	96352241	96352241	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr10:96352241G>A	ENST00000348459.5	+	17	2046	c.1941G>A	c.(1939-1941)ggG>ggA	p.G647G	RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000394045.1_Silent_p.G549G|HELLS_ENST00000371332.4_Silent_p.G693G|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000394036.1_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GGCTTGATGGGTCCATGTCTT	0.343																																																0													89.0	89.0	89.0					10																	96352241		2203	4300	6503	SO:0001819	synonymous_variant	3070			AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"""SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6"", ""proliferation-associated SNF2-like protein"""	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1941G>A	10.37:g.96352241G>A				Silent	SNP	ENST00000348459.5	37	CCDS7434.1																																																																																				0.343	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		12	44	12	44
SLIT1	6585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	98764460	98764460	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr10:98764460C>T	ENST00000266058.4	-	33	3945	c.3700G>A	c.(3700-3702)Gcc>Acc	p.A1234T	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.A1234T	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1234	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CTGTAGATGGCAGAGCTGGGG	0.602																																																0													181.0	143.0	156.0					10																	98764460		2203	4300	6503	SO:0001583	missense	6585			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.3700G>A	10.37:g.98764460C>T	ENSP00000266058:p.Ala1234Thr		Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	8.868	0.948539	0.18356	.	.	ENSG00000187122	ENST00000266058;ENST00000371070	T;T	0.68903	-0.36;-0.36	4.38	4.38	0.52667	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.155015	0.56097	D	0.000022	T	0.41282	0.1152	N	0.04355	-0.22	0.80722	D	1	B	0.25272	0.122	B	0.22152	0.038	T	0.45848	-0.9233	10	0.02654	T	1	.	17.1657	0.86816	0.0:1.0:0.0:0.0	.	1234	O75093	SLIT1_HUMAN	T	1234	ENSP00000266058:A1234T;ENSP00000360109:A1234T	ENSP00000266058:A1234T	A	-	1	0	SLIT1	98754450	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.774000	0.62339	2.271000	0.75665	0.555000	0.69702	GCC		0.602	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		15	65	15	65
MAP3K12	7786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	53877509	53877509	+	Splice_Site	SNP	T	T	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr12:53877509T>A	ENST00000267079.2	-	10	1485		c.e10-2		MAP3K12_ENST00000547151.1_5'Flank|MAP3K12_ENST00000547035.1_Splice_Site|MAP3K12_ENST00000547488.1_Splice_Site	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12						histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						AGGGCGTGTCTGCAACGGGCA	0.507																																																0													105.0	92.0	97.0					12																	53877509		2203	4300	6503	SO:0001630	splice_region_variant	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.1260-2A>T	12.37:g.53877509T>A			B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Splice_Site	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658558	0.67586	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	.	.	.	5.12	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0221	0.42048	0.0:0.0806:0.0:0.9194	.	.	.	.	.	-1	.	.	.	-	.	.	MAP3K12	52163776	1.000000	0.71417	0.995000	0.50966	0.872000	0.50106	7.843000	0.86859	1.096000	0.41439	0.533000	0.62120	.		0.507	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301	Intron	8	64	8	64
SMUG1	23583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	54577582	54577582	+	Missense_Mutation	SNP	G	G	A	rs149806805		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr12:54577582G>A	ENST00000508394.2	-	2	205	c.143C>T	c.(142-144)tCg>tTg	p.S48L	SMUG1_ENST00000505128.1_Missense_Mutation_p.S48L|SMUG1_ENST00000506595.1_Missense_Mutation_p.S48L|SMUG1_ENST00000514685.1_Missense_Mutation_p.S48L|SMUG1_ENST00000513838.1_Missense_Mutation_p.S48L|SMUG1_ENST00000401977.2_Missense_Mutation_p.S48L|SMUG1_ENST00000337581.3_Missense_Mutation_p.S48L|SMUG1_ENST00000505662.1_5'UTR|SMUG1_ENST00000514196.1_Missense_Mutation_p.S48L|SMUG1_ENST00000243112.5_Missense_Mutation_p.S48L	NM_001243787.1|NM_001243788.1|NM_014311.2	NP_001230716.1|NP_001230717.1|NP_055126.1	Q53HV7	SMUG1_HUMAN	single-strand-selective monofunctional uracil-DNA glycosylase 1	48				S -> L (in Ref. 3; BAC03670). {ECO:0000305}.	base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA N-glycosylase activity (GO:0019104)|oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity (GO:0000703)|single-strand selective uracil DNA N-glycosylase activity (GO:0017065)|uracil DNA N-glycosylase activity (GO:0004844)			kidney(1)|large_intestine(4)|lung(1)	6						CACAGGCTCCGAAAACTGCAG	0.597								Base excision repair (BER), DNA glycosylases					G|||	1	0.000199681	0.0	0.0	5008	,	,		19629	0.0		0.001	False		,,,				2504	0.0															0								G	LEU/SER	4,4402	8.1+/-20.4	0,4,2199	69.0	61.0	64.0		143	3.0	0.1	12	dbSNP_134	64	9,8591	6.4+/-24.3	0,9,4291	yes	missense	SMUG1	NM_014311.2	145	0,13,6490	AA,AG,GG		0.1047,0.0908,0.1	benign	48/271	54577582	13,12993	2203	4300	6503	SO:0001583	missense	23583			AF125182	CCDS8874.1, CCDS58239.1	12q13.13	2013-10-28			ENSG00000123415	ENSG00000123415			17148	protein-coding gene	gene with protein product		607753				10074426, 11526119	Standard	NM_014311		Approved	UNG3, FDG, HMUDG	uc009znf.2	Q53HV7	OTTHUMG00000160068	ENST00000508394.2:c.143C>T	12.37:g.54577582G>A	ENSP00000424191:p.Ser48Leu		A8K2K9|O95862|Q0D2M0|Q8NB71|Q9BWC8	Missense_Mutation	SNP	ENST00000508394.2	37	CCDS8874.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.925	1.213169	0.22289	9.08E-4	0.001047	ENSG00000123415	ENST00000506595;ENST00000514685;ENST00000505128;ENST00000337581;ENST00000508394;ENST00000513838;ENST00000243112;ENST00000401977;ENST00000514196;ENST00000504338;ENST00000507904;ENST00000503447;ENST00000504797;ENST00000506169;ENST00000503306	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	4.85	3.03	0.35002	Uracil-DNA glycosylase-like (2);	0.496492	0.22912	N	0.054127	T	0.44201	0.1282	M	0.76574	2.34	0.09310	N	1	P;D;B	0.60160	0.585;0.987;0.116	B;P;B	0.47891	0.078;0.56;0.017	T	0.34354	-0.9832	10	0.37606	T	0.19	.	5.7828	0.18316	0.1658:0.0:0.6794:0.1549	.	48;48;48	Q53HV7;D6RAI1;Q53HV7-2	SMUG1_HUMAN;.;.	L	48	ENSP00000421206:S48L;ENSP00000421139:S48L;ENSP00000421894:S48L;ENSP00000338606:S48L;ENSP00000424191:S48L;ENSP00000423629:S48L;ENSP00000243112:S48L;ENSP00000384828:S48L;ENSP00000425974:S48L;ENSP00000423083:S48L;ENSP00000423457:S48L;ENSP00000421790:S48L;ENSP00000427547:S48L;ENSP00000425426:S48L	ENSP00000243112:S48L	S	-	2	0	SMUG1	52863849	0.988000	0.35896	0.056000	0.19401	0.566000	0.35808	2.715000	0.47210	0.765000	0.33221	-0.229000	0.12294	TCG		0.597	SMUG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359074.3	NM_014311		6	55	6	55
TBX5	6910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	114793348	114793348	+	Missense_Mutation	SNP	C	C	T	rs200354838		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr12:114793348C>T	ENST00000310346.4	-	9	2212	c.1546G>A	c.(1546-1548)Gac>Aac	p.D516N	TBX5_ENST00000405440.2_Missense_Mutation_p.D516N|TBX5_ENST00000349716.5_Missense_Mutation_p.D466N	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	516				PRTLSPHQYHSVHGVGMVPEWSDNS -> QGLYPLISTTLC TELAWCRVERQ (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		TAGCTATTGTCGCTCCACTCT	0.517													C|||	1	0.000199681	0.0	0.0014	5008	,	,		21402	0.0		0.0	False		,,,				2504	0.0				NSCLC(152;1358 1980 4050 23898 40356)											0													43.0	42.0	42.0					12																	114793348		2203	4300	6503	SO:0001583	missense	6910			U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1546G>A	12.37:g.114793348C>T	ENSP00000309913:p.Asp516Asn		A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.92	2.974859	0.53720	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000405440	D;D;D	0.88975	-2.4;-2.45;-2.45	5.42	4.51	0.55191	.	0.589818	0.18864	N	0.129055	D	0.82342	0.5016	N	0.24115	0.695	0.80722	D	1	B	0.25105	0.118	B	0.14023	0.01	T	0.79022	-0.1973	10	0.72032	D	0.01	.	15.2177	0.73281	0.1418:0.8582:0.0:0.0	.	516	Q99593	TBX5_HUMAN	N	466;516;516	ENSP00000337723:D466N;ENSP00000309913:D516N;ENSP00000384152:D516N	ENSP00000309913:D516N	D	-	1	0	TBX5	113277731	1.000000	0.71417	0.220000	0.23810	0.623000	0.37688	7.487000	0.81328	1.230000	0.43646	0.655000	0.94253	GAC		0.517	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		8	56	8	56
TRPM1	4308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	31359319	31359319	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr15:31359319C>T	ENST00000256552.6	-	6	712	c.565G>A	c.(565-567)Gga>Aga	p.G189R	TRPM1_ENST00000397795.2_Missense_Mutation_p.G167R|TRPM1_ENST00000542188.1_Missense_Mutation_p.G206R|MIR211_ENST00000384969.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GGAGCAATTCCTATAGCACAA	0.453																																																0													114.0	112.0	113.0					15																	31359319		1889	4114	6003	SO:0001583	missense	4308			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.565G>A	15.37:g.31359319C>T	ENSP00000256552:p.Gly189Arg			Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	35	5.507972	0.96386	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.18016	2.24;2.24;2.24	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.56834	0.2012	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.65726	-0.6098	10	0.87932	D	0	-29.4806	20.7342	0.99715	0.0:1.0:0.0:0.0	.	167;167	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	R	167;206;189;167	ENSP00000380897:G167R;ENSP00000437849:G206R;ENSP00000256552:G189R	ENSP00000256552:G189R	G	-	1	0	TRPM1	29146611	1.000000	0.71417	0.910000	0.35882	0.997000	0.91878	7.795000	0.85887	2.906000	0.99361	0.655000	0.94253	GGA		0.453	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		50	74	50	74
SPPL2A	84888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	51017471	51017471	+	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr15:51017471C>G	ENST00000261854.5	-	12	1470	c.1196G>C	c.(1195-1197)aGt>aCt	p.S399T	SPPL2A_ENST00000559293.1_5'UTR	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	399					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		GAGGCACACACTCATTACTGA	0.313																																					Melanoma(50;790 1209 4069 22965 33125)											0													109.0	107.0	108.0					15																	51017471		2196	4294	6490	SO:0001583	missense	84888				CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1196G>C	15.37:g.51017471C>G	ENSP00000261854:p.Ser399Thr		B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	37	CCDS10138.1	.	.	.	.	.	.	.	.	.	.	C	5.496	0.276493	0.10403	.	.	ENSG00000138600	ENST00000261854	T	0.12039	2.72	5.43	3.42	0.39159	.	0.202695	0.49305	D	0.000142	T	0.05227	0.0139	N	0.04116	-0.275	0.28057	N	0.933145	B	0.21688	0.059	B	0.19666	0.026	T	0.38067	-0.9678	10	0.10111	T	0.7	-6.0168	8.5216	0.33279	0.0:0.5767:0.3331:0.0903	.	399	Q8TCT8	PSL2_HUMAN	T	399	ENSP00000261854:S399T	ENSP00000261854:S399T	S	-	2	0	AC012100.1	48804763	0.996000	0.38824	1.000000	0.80357	0.991000	0.79684	1.334000	0.33827	1.279000	0.44446	0.557000	0.71058	AGT		0.313	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		52	120	52	120
TPM1	7168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	63336271	63336271	+	Missense_Mutation	SNP	G	G	A	rs104894505		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr15:63336271G>A	ENST00000403994.3	+	2	240	c.160G>A	c.(160-162)Gaa>Aaa	p.E54K	TPM1_ENST00000358278.3_Missense_Mutation_p.E54K|TPM1_ENST00000560445.1_Missense_Mutation_p.E54K|TPM1_ENST00000357980.4_Missense_Mutation_p.E96K|TPM1_ENST00000267996.7_Intron|TPM1_ENST00000559556.1_Missense_Mutation_p.E54K|TPM1_ENST00000559397.1_Intron|RP11-244F12.3_ENST00000561241.1_RNA|TPM1_ENST00000288398.6_Missense_Mutation_p.E54K	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	54			E -> K (in CMD1Y). {ECO:0000269|PubMed:11273725}.		cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						CAAGGGCACCGAAGATGAACT	0.562																																																0			GRCh37	CM014116	TPM1	M	rs104894505						60.0	57.0	58.0					15																	63336271		2203	4300	6503	SO:0001583	missense	7168			AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.160G>A	15.37:g.63336271G>A	ENSP00000385107:p.Glu54Lys		B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000403994.3	37	CCDS45273.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.145333	0.77888	.	.	ENSG00000140416	ENST00000288398;ENST00000358278;ENST00000403994;ENST00000357980	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	5.82	5.82	0.92795	.	0.000000	0.52532	D	0.000072	D	0.86648	0.5983	L	0.53617	1.68	0.80722	D	1	P;P;P;B;B;P	0.52061	0.923;0.95;0.866;0.272;0.393;0.923	P;P;P;P;P;P	0.58970	0.849;0.609;0.752;0.693;0.483;0.849	D	0.86654	0.1900	10	0.62326	D	0.03	-16.2738	19.0927	0.93233	0.0:0.0:1.0:0.0	.	54;96;54;54;54;54	D9YZV4;Q6ZN40;D9YZV5;D9YZV3;D9YZV2;P09493	.;.;.;.;.;TPM1_HUMAN	K	54;54;54;96	ENSP00000288398:E54K;ENSP00000351022:E54K;ENSP00000385107:E54K;ENSP00000350667:E96K	ENSP00000288398:E54K	E	+	1	0	TPM1	61123324	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	9.435000	0.97529	2.759000	0.94783	0.561000	0.74099	GAA		0.562	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004		9	25	9	25
NEO1	4756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	73428355	73428355	+	Missense_Mutation	SNP	G	G	C			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr15:73428355G>C	ENST00000339362.5	+	6	1449	c.1002G>C	c.(1000-1002)gaG>gaC	p.E334D	NEO1_ENST00000560262.1_Missense_Mutation_p.E334D|NEO1_ENST00000558964.1_Missense_Mutation_p.E334D|NEO1_ENST00000261908.6_Missense_Mutation_p.E334D			Q92859	NEO1_HUMAN	neogenin 1	334	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CTCAAGCAGAGCTTACAGTGC	0.373																																																0													113.0	110.0	111.0					15																	73428355		2198	4297	6495	SO:0001583	missense	4756			U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1002G>C	15.37:g.73428355G>C	ENSP00000341198:p.Glu334Asp		B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.467306	0.26335	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.69435	-0.4;-0.4	6.04	2.44	0.29823	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.220802	0.46442	D	0.000295	T	0.42585	0.1209	N	0.20530	0.585	0.40268	D	0.978255	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.001;0.004	T	0.21861	-1.0233	10	0.18276	T	0.48	-20.4676	4.7015	0.12828	0.2379:0.2583:0.5038:0.0	.	334;334;334	B7ZKM9;B7ZKN0;Q92859	.;.;NEO1_HUMAN	D	334;52;334	ENSP00000341198:E334D;ENSP00000261908:E334D	ENSP00000261908:E334D	E	+	3	2	NEO1	71215408	0.995000	0.38212	0.995000	0.50966	0.446000	0.32137	0.194000	0.17135	1.568000	0.49683	0.561000	0.74099	GAG		0.373	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		17	32	17	32
SMAD2	4087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	45422914	45422914	+	Missense_Mutation	SNP	T	T	C			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr18:45422914T>C	ENST00000402690.2	-	2	608	c.214A>G	c.(214-216)Act>Gct	p.T72A	SMAD2_ENST00000356825.4_Missense_Mutation_p.T72A|SMAD2_ENST00000586040.1_Missense_Mutation_p.T72A|SMAD2_ENST00000591214.1_Missense_Mutation_p.T72A|SMAD2_ENST00000262160.6_Missense_Mutation_p.T72A	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	72	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|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)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						ACACATTTAGTATTACAGTTT	0.368																																																0													227.0	210.0	216.0					18																	45422914		2203	4300	6503	SO:0001583	missense	4087			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"""SMADs"""	6768	protein-coding gene	gene with protein product		601366	"""MAD, mothers against decapentaplegic homolog 2 (Drosophila)"", ""SMAD, mothers against DPP homolog 2 (Drosophila)"""	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.214A>G	18.37:g.45422914T>C	ENSP00000384449:p.Thr72Ala			Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173458	0.78452	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	T;T;T	0.76578	-1.03;-1.03;-1.03	5.36	4.18	0.49190	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.79475	2.455	0.58432	D	0.999999	P;P;D	0.76494	0.868;0.906;0.999	P;P;D	0.79108	0.803;0.702;0.992	D	0.87919	0.2702	10	0.87932	D	0	.	12.7762	0.57451	0.0:0.0:0.137:0.863	.	72;72;72	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	A	72	ENSP00000262160:T72A;ENSP00000349282:T72A;ENSP00000384449:T72A	ENSP00000262160:T72A	T	-	1	0	SMAD2	43676912	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	0.959000	0.37980	0.454000	0.30748	ACT		0.368	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		9	86	9	86
DAPK3	1613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	3964722	3964722	+	Silent	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:3964722C>T	ENST00000545797.2	-	3	573	c.330G>A	c.(328-330)tcG>tcA	p.S110S	DAPK3_ENST00000301264.3_Silent_p.S110S			O43293	DAPK3_HUMAN	death-associated protein kinase 3	110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCCGTCAGCGACTCCTTCT	0.592																																																0													110.0	108.0	108.0					19																	3964722		2203	4300	6503	SO:0001819	synonymous_variant	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.330G>A	19.37:g.3964722C>T			A0AVN4|B3KQE2|Q05JY4	Silent	SNP	ENST00000545797.2	37	CCDS12116.1																																																																																				0.592	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2	NM_001348		17	133	17	133
C3	718	hgsc.bcm.edu;broad.mit.edu	37	19	6718386	6718386	+	Missense_Mutation	SNP	C	C	T	rs554587967		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:6718386C>T	ENST00000245907.6	-	3	397	c.305G>A	c.(304-306)cGc>cAc	p.R102H		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	102			R -> G (in allele C3F; associated with susceptibility to ARMD9; results in decreased binding affinity for regulator factor H; results in reduced sensitivity to cleavage by factor I; dbSNP:rs2230199). {ECO:0000269|PubMed:1976733, ECO:0000269|Ref.2}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GAACTTGTTGCGCCCCTTTTC	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0															0													130.0	112.0	118.0					19																	6718386		2203	4300	6503	SO:0001583	missense	718			J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.305G>A	19.37:g.6718386C>T	ENSP00000245907:p.Arg102His		A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	C	2.367	-0.345186	0.05208	.	.	ENSG00000125730	ENST00000245907	T	0.32988	1.43	0.189	-0.378	0.12497	.	4.761290	0.00397	N	0.000045	T	0.09949	0.0244	N	0.00621	-1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14559	-1.0468	9	0.46703	T	0.11	.	.	.	.	.	102	P01024	CO3_HUMAN	H	102	ENSP00000245907:R102H	ENSP00000245907:R102H	R	-	2	0	C3	6669386	0.016000	0.18221	0.000000	0.03702	0.040000	0.13550	0.878000	0.28126	-0.843000	0.04189	-0.849000	0.03036	CGC		0.607	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		10	148	10	148
ZNF878	729747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	12154973	12154973	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:12154973G>A	ENST00000547628.1	-	4	1380	c.1243C>T	c.(1243-1245)Cga>Tga	p.R415*	CTD-2006C1.10_ENST00000547473.1_Intron|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000591838.1_RNA|ZNF878_ENST00000602107.1_Nonsense_Mutation_p.R462*	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GTGTGAGTTCGTATGTGCTTT	0.433																																																0													73.0	76.0	75.0					19																	12154973		2202	4300	6502	SO:0001587	stop_gained	729747				CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"""Zinc fingers, C2H2-type"", ""-"""	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.1243C>T	19.37:g.12154973G>A	ENSP00000447931:p.Arg415*			Nonsense_Mutation	SNP	ENST00000547628.1	37	CCDS45984.2	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891095	0.91889	.	.	ENSG00000257446;ENSG00000232371	ENST00000547628;ENST00000440730	.	.	.	1.3	-0.0775	0.13718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.7589	0.05300	0.0:0.3527:0.2838:0.3635	.	.	.	.	X	415;462	.	ENSP00000447931:R415X	R	-	1	2	AC022415.4;ZNF878	12015973	0.000000	0.05858	0.001000	0.08648	0.836000	0.47400	-2.681000	0.00837	-0.261000	0.09405	-0.823000	0.03104	CGA		0.433	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404		13	34	13	34
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	15299837	15299837	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:15299837G>A	ENST00000263388.2	-	8	1416	c.1341C>T	c.(1339-1341)ctC>ctT	p.L447L		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	447	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CTATGCGGTCGAGGCACGTGG	0.667																																																0													31.0	26.0	28.0					19																	15299837		2203	4300	6503	SO:0001819	synonymous_variant	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1341C>T	19.37:g.15299837G>A			Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																				0.667	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		9	32	9	32
TEAD2	8463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	49845721	49845721	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:49845721C>T	ENST00000311227.2	-	11	1294	c.1204G>A	c.(1204-1206)Gtc>Atc	p.V402I	TEAD2_ENST00000601519.1_Missense_Mutation_p.V405I|TEAD2_ENST00000539846.1_Missense_Mutation_p.V274I|TEAD2_ENST00000593945.1_Missense_Mutation_p.V406I|CTC-301O7.4_ENST00000358234.4_lincRNA|TEAD2_ENST00000377214.4_Missense_Mutation_p.V405I|TEAD2_ENST00000598810.1_Missense_Mutation_p.V406I	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	402	Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TTTTCCAGGACGCTGTTCATC	0.572																																																0													72.0	68.0	69.0					19																	49845721		2203	4300	6503	SO:0001583	missense	8463			X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.1204G>A	19.37:g.49845721C>T	ENSP00000310701:p.Val402Ile		B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	37	CCDS12761.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.981683	0.74474	.	.	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.35421	1.31;1.31;1.31	3.9	2.85	0.33270	.	0.111684	0.37219	N	0.002185	T	0.36771	0.0979	M	0.74881	2.28	0.58432	D	0.999996	P;B;B	0.43662	0.814;0.41;0.172	B;B;B	0.38985	0.195;0.287;0.034	T	0.39482	-0.9612	10	0.87932	D	0	-30.8716	9.9379	0.41563	0.0:0.8944:0.0:0.1056	.	274;402;405	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	I	402;405;274	ENSP00000310701:V402I;ENSP00000366419:V405I;ENSP00000437928:V274I	ENSP00000310701:V402I	V	-	1	0	TEAD2	54537533	1.000000	0.71417	0.999000	0.59377	0.852000	0.48524	6.021000	0.70832	0.950000	0.37743	-0.192000	0.12808	GTC		0.572	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598		27	35	27	35
U2AF2	11338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	56175034	56175034	+	Missense_Mutation	SNP	G	G	C			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:56175034G>C	ENST00000308924.4	+	7	706	c.666G>C	c.(664-666)caG>caC	p.Q222H	U2AF2_ENST00000590551.1_Missense_Mutation_p.Q58H|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000450554.2_Missense_Mutation_p.Q222H|CTD-2537I9.12_ENST00000589456.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	222	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TCCAGGGCCAGTCACTAAAGA	0.567																																																0													153.0	133.0	140.0					19																	56175034		2203	4300	6503	SO:0001583	missense	11338			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.666G>C	19.37:g.56175034G>C	ENSP00000307863:p.Gln222His		Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810831	0.70797	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.07908	3.15;3.15	4.0	1.85	0.25348	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.15739	0.0379	L	0.42008	1.315	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.982	T	0.11155	-1.0599	10	0.14656	T	0.56	-31.4239	10.0282	0.42085	0.1836:0.0:0.8164:0.0	.	222;222	P26368;P26368-2	U2AF2_HUMAN;.	H	222	ENSP00000307863:Q222H;ENSP00000388475:Q222H	ENSP00000307863:Q222H	Q	+	3	2	U2AF2	60866846	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.053000	0.57427	1.025000	0.39708	0.655000	0.94253	CAG		0.567	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		10	106	10	106
PRRC2C	23215	hgsc.bcm.edu;broad.mit.edu	37	1	171511013	171511013	+	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr1:171511013C>G	ENST00000338920.4	+	16	4639	c.4402C>G	c.(4402-4404)Cca>Gca	p.P1468A	PRRC2C_ENST00000392078.3_Missense_Mutation_p.P1470A|PRRC2C_ENST00000426496.2_Missense_Mutation_p.P1468A|PRRC2C_ENST00000367742.3_Missense_Mutation_p.P1470A	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1468					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GGCTCAAGAACCAGTTAATAC	0.428																																																0													65.0	64.0	65.0					1																	171511013		2203	4300	6503	SO:0001583	missense	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4402C>G	1.37:g.171511013C>G	ENSP00000343629:p.Pro1468Ala		Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.390|5.390	0.257260|0.257260	0.10239|0.10239	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.01902	.|4.57;4.57;4.57;4.57	5.65|5.65	3.75|3.75	0.43078|0.43078	.|.	.|0.486257	.|0.17239	.|N	.|0.181625	T|T	0.00724|0.00724	0.0024|0.0024	L|L	0.47716|0.47716	1.5|1.5	0.32127|0.32127	N|N	0.587211|0.587211	.|B	.|0.02656	.|0.0	.|B	.|0.08055	.|0.003	T|T	0.45498|0.45498	-0.9257|-0.9257	5|10	.|0.02654	.|T	.|1	.|.	11.67|11.67	0.51395|0.51395	0.0:0.7988:0.1332:0.0679|0.0:0.7988:0.1332:0.0679	.|.	.|1468	.|Q9Y520-4	.|.	K|A	15|1470;1469;1468;1470;1468;1225	.|ENSP00000375928:P1470A;ENSP00000410219:P1468A;ENSP00000356716:P1470A;ENSP00000343629:P1468A	.|ENSP00000343629:P1468A	N|P	+|+	3|1	2|0	PRRC2C|PRRC2C	169777637|169777637	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.807000|0.807000	0.45602|0.45602	1.194000|1.194000	0.32174|0.32174	0.710000|0.710000	0.31997|0.31997	0.650000|0.650000	0.86243|0.86243	AAC|CCA		0.428	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		5	61	5	61
BPIFB3	359710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	31659936	31659936	+	Silent	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr20:31659936C>T	ENST00000375494.3	+	13	1287	c.1287C>T	c.(1285-1287)agC>agT	p.S429S		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	429					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										AATGGCTCAGCCATGTGGTCG	0.532																																																0													193.0	134.0	154.0					20																	31659936		2203	4300	6503	SO:0001819	synonymous_variant	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1287C>T	20.37:g.31659936C>T			Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																				0.532	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		15	87	15	87
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu	37	21	46909433	46909433	+	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr21:46909433A>G	ENST00000359759.4	+	18	3223	c.3202A>G	c.(3202-3204)Aag>Gag	p.K1068E	COL18A1_ENST00000355480.5_Missense_Mutation_p.K833E|COL18A1_ENST00000400337.2_Missense_Mutation_p.K653E			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1068	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCCGGGGGCGAAGGTAAGCGC	0.706																																																0													13.0	17.0	15.0					21																	46909433		1983	4130	6113	SO:0001583	missense	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3202A>G	21.37:g.46909433A>G	ENSP00000352798:p.Lys1068Glu		A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	A	15.71	2.914208	0.52546	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.96522	-4.04;-4.04;-4.04	3.74	3.74	0.42951	.	0.000000	0.64402	U	0.000001	D	0.96402	0.8826	L	0.54908	1.71	0.44946	D	0.997963	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.79108	0.992;0.986;0.986	D	0.94154	0.7408	10	0.20046	T	0.44	.	9.0481	0.36358	1.0:0.0:0.0:0.0	.	1068;833;653	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	E	653;653;833;1068;1068	ENSP00000383191:K653E;ENSP00000347665:K833E;ENSP00000352798:K1068E	ENSP00000347665:K833E	K	+	1	0	COL18A1	45733861	0.757000	0.28394	0.695000	0.30226	0.061000	0.15899	1.204000	0.32296	1.710000	0.51325	0.528000	0.53228	AAG		0.706	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			10	12	10	12
PARVB	29780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	44489821	44489821	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr22:44489821G>A	ENST00000338758.7	+	2	189	c.126G>A	c.(124-126)caG>caA	p.Q42Q	PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000406477.3_Silent_p.Q75Q|PARVB_ENST00000404989.1_Silent_p.Q5Q	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	42					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GTGACCTGCAGGAAGAAGGCA	0.547																																																0													110.0	109.0	109.0					22																	44489821		2203	4300	6503	SO:0001819	synonymous_variant	29780			AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.126G>A	22.37:g.44489821G>A			B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	37	CCDS14056.1																																																																																				0.547	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		49	104	49	104
TTN	7273	hgsc.bcm.edu;broad.mit.edu	37	2	179634978	179634978	+	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr2:179634978C>G	ENST00000591111.1	-	36	8674	c.8450G>C	c.(8449-8451)aGt>aCt	p.S2817T	TTN_ENST00000342992.6_Missense_Mutation_p.S2817T|TTN_ENST00000359218.5_Missense_Mutation_p.S2771T|TTN_ENST00000460472.2_Missense_Mutation_p.S2771T|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.S2817T|TTN_ENST00000589042.1_Missense_Mutation_p.S2817T|TTN_ENST00000342175.6_Missense_Mutation_p.S2771T|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13145					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGGGAAACACTAACTTCAAA	0.408																																																0													161.0	154.0	156.0					2																	179634978		2203	4300	6503	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8450G>C	2.37:g.179634978C>G	ENSP00000465570:p.Ser2817Thr		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	15.69	2.907887	0.52333	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12	6.06	6.06	0.98353	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70509	0.3232	N	0.21545	0.675	0.37366	D	0.911436	D;D;D;D;D	0.76494	0.989;0.989;0.989;0.994;0.999	P;P;P;D;D	0.70935	0.87;0.87;0.87;0.926;0.971	T	0.75105	-0.3435	9	0.87932	D	0	.	20.6282	0.99521	0.0:1.0:0.0:0.0	.	2771;2771;2771;2817;2817	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	2817;2771;2771;2771;2771;2817	ENSP00000343764:S2817T;ENSP00000434586:S2771T;ENSP00000340554:S2771T;ENSP00000352154:S2771T;ENSP00000354117:S2817T	ENSP00000340554:S2771T	S	-	2	0	TTN	179343223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.686000	0.68211	2.871000	0.98454	0.655000	0.94253	AGT		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		8	95	8	95
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	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			20	65	20	65
NGEF	25791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	233759484	233759484	+	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr2:233759484A>G	ENST00000264051.3	-	6	1249	c.971T>C	c.(970-972)gTg>gCg	p.V324A	NGEF_ENST00000373552.4_Missense_Mutation_p.V232A|NGEF_ENST00000539537.1_Missense_Mutation_p.V47A|NGEF_ENST00000409079.1_Missense_Mutation_p.V232A	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	324	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		GACAGCCAGCACGTCCAGGAC	0.602																																																0													79.0	71.0	74.0					2																	233759484		2203	4300	6503	SO:0001583	missense	25791			AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.971T>C	2.37:g.233759484A>G	ENSP00000264051:p.Val324Ala		B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	37	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.896335	0.91962	.	.	ENSG00000066248	ENST00000264051;ENST00000373552;ENST00000541023;ENST00000539537;ENST00000416114;ENST00000458735;ENST00000409079	T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41	5.22	5.22	0.72569	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.89095	3.005	0.80722	D	1	D;D;D	0.76494	0.979;0.99;0.999	D;P;D	0.72625	0.956;0.897;0.978	T	0.70644	-0.4815	10	0.87932	D	0	-46.3681	15.1186	0.72423	1.0:0.0:0.0:0.0	.	232;232;324	E9PC42;B4DMB8;Q8N5V2	.;.;NGEF_HUMAN	A	324;232;214;47;47;47;232	ENSP00000264051:V324A;ENSP00000362653:V232A;ENSP00000439035:V47A;ENSP00000401063:V47A;ENSP00000412614:V47A;ENSP00000387033:V232A	ENSP00000264051:V324A	V	-	2	0	NGEF	233467728	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	8.917000	0.92751	1.976000	0.57569	0.533000	0.62120	GTG		0.602	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		31	82	31	82
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	58097875	58097875	+	Splice_Site	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr3:58097875G>A	ENST00000295956.4	+	18	2740		c.e18-1		FLNB_ENST00000358537.3_Splice_Site|FLNB_ENST00000493452.1_Splice_Site|FLNB_ENST00000357272.4_Splice_Site|FLNB_ENST00000348383.5_Splice_Site|FLNB_ENST00000419752.2_Splice_Site|FLNB_ENST00000490882.1_Splice_Site|FLNB_ENST00000429972.2_Splice_Site	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta						actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TATCTTTCCAGGTGTGGAAAA	0.522																																																0													105.0	110.0	108.0					3																	58097875		2203	4300	6503	SO:0001630	splice_region_variant	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2576-1G>A	3.37:g.58097875G>A			B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Splice_Site	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.883139	0.91740	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9418	0.92608	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FLNB	58072915	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.866000	0.99616	2.488000	0.83962	0.655000	0.94253	.		0.522	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	Intron	83	137	83	137
CRYBG3	131544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	97596597	97596597	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr3:97596597C>T	ENST00000182096.4	+	1	779	c.715C>T	c.(715-717)Cag>Tag	p.Q239*		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2187							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						CCCTGATGACCAGGAGAGCGT	0.468																																																0													73.0	75.0	74.0					3																	97596597		2019	4195	6214	SO:0001587	stop_gained	131544					3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.715C>T	3.37:g.97596597C>T	ENSP00000182096:p.Gln239*		B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Nonsense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	C	19.74	3.883429	0.72410	.	.	ENSG00000080200	ENST00000182096	.	.	.	5.44	5.44	0.79542	.	1.728010	0.02823	N	0.125765	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	13.978	0.64285	0.0:0.8488:0.1512:0.0	.	.	.	.	X	239	.	ENSP00000182096:Q239X	Q	+	1	0	CRYBG3	99079287	0.991000	0.36638	1.000000	0.80357	0.167000	0.22549	1.107000	0.31110	2.564000	0.86499	0.555000	0.69702	CAG		0.468	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		12	22	12	22
ENAM	10117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	71508741	71508741	+	Missense_Mutation	SNP	C	C	T	rs576885761	byFrequency	TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr4:71508741C>T	ENST00000396073.3	+	9	1879	c.1598C>T	c.(1597-1599)aCt>aTt	p.T533I	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	533					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			GAATCAGAAACTAATCAGTCA	0.413																																																0													93.0	93.0	93.0					4																	71508741		2203	4300	6503	SO:0001583	missense	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1598C>T	4.37:g.71508741C>T	ENSP00000379383:p.Thr533Ile		Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	C	4.769	0.142960	0.09083	.	.	ENSG00000132464	ENST00000396073	T	0.34472	1.36	5.93	2.75	0.32379	.	0.202600	0.35525	N	0.003151	T	0.27098	0.0664	L	0.52364	1.645	0.30336	N	0.786158	B	0.29671	0.254	B	0.32022	0.139	T	0.10847	-1.0612	10	0.29301	T	0.29	-9.7108	3.7285	0.08484	0.1902:0.5961:0.0:0.2137	.	533	Q9NRM1	ENAM_HUMAN	I	533	ENSP00000379383:T533I	ENSP00000379383:T533I	T	+	2	0	ENAM	71727605	0.871000	0.30034	0.998000	0.56505	0.205000	0.24178	0.741000	0.26202	1.418000	0.47098	0.655000	0.94253	ACT		0.413	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		32	63	32	63
NAF1	92345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	164050323	164050323	+	Missense_Mutation	SNP	T	T	C			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr4:164050323T>C	ENST00000274054.2	-	8	1404	c.1211A>G	c.(1210-1212)cAg>cGg	p.Q404R	NAF1_ENST00000422287.2_Intron|NAF1_ENST00000509434.1_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	404					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				TGAAGTCTCCTGAGATACCAT	0.458																																																0													87.0	95.0	93.0					4																	164050323		2203	4300	6503	SO:0001583	missense	92345				CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.1211A>G	4.37:g.164050323T>C	ENSP00000274054:p.Gln404Arg		D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	T	8.744	0.919573	0.17982	.	.	ENSG00000145414	ENST00000274054	T	0.43688	0.94	4.38	0.0493	0.14289	.	0.560968	0.18627	N	0.135681	T	0.25644	0.0624	L	0.32530	0.975	0.28218	N	0.926659	B	0.29909	0.261	B	0.29353	0.101	T	0.13926	-1.0491	10	0.27082	T	0.32	-3.7229	6.0716	0.19893	0.1532:0.0:0.3103:0.5365	.	404	Q96HR8	NAF1_HUMAN	R	404	ENSP00000274054:Q404R	ENSP00000274054:Q404R	Q	-	2	0	NAF1	164269773	0.993000	0.37304	0.182000	0.23118	0.206000	0.24218	1.556000	0.36288	-0.058000	0.13177	0.482000	0.46254	CAG		0.458	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		10	50	10	50
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	187521295	187521295	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr4:187521295C>T	ENST00000441802.2	-	22	12069	c.11860G>A	c.(11860-11862)Ggc>Agc	p.G3954S	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3954	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CGGATGTGGCCACCAAAAAAC	0.483										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)											0													102.0	103.0	103.0					4																	187521295		1976	4148	6124	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11860G>A	4.37:g.187521295C>T	ENSP00000406229:p.Gly3954Ser			Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	31	5.065625	0.93898	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	D	0.86562	-2.14	4.94	4.94	0.65067	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.052190	0.85682	D	0.000000	D	0.93723	0.7994	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93775	0.7078	10	0.56958	D	0.05	.	18.7161	0.91677	0.0:1.0:0.0:0.0	.	3954	Q14517	FAT1_HUMAN	S	3954;3956	ENSP00000406229:G3954S	ENSP00000260147:G3956S	G	-	1	0	FAT1	187758289	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.490000	0.81461	2.726000	0.93360	0.655000	0.94253	GGC		0.483	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		6	46	6	46
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	179192669	179192669	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr5:179192669C>T	ENST00000292599.3	+	2	921	c.658C>T	c.(658-660)Cct>Tct	p.P220S	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGCAGGAGCCTGTCGAAGA	0.517																																																0													68.0	59.0	62.0					5																	179192669		2203	4300	6503	SO:0001583	missense	9794			D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.658C>T	5.37:g.179192669C>T	ENSP00000292599:p.Pro220Ser			Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934797	0.73442	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	T	0.48201	0.82	4.9	4.9	0.64082	.	0.000000	0.64402	D	0.000001	T	0.69993	0.3173	M	0.78637	2.42	0.80722	D	1	D;D	0.69078	0.994;0.997	D;D	0.71414	0.966;0.973	T	0.75371	-0.3341	10	0.87932	D	0	-11.3637	18.0605	0.89375	0.0:1.0:0.0:0.0	.	257;220	Q59GH4;Q92585	.;MAML1_HUMAN	S	220;257	ENSP00000292599:P220S	ENSP00000292599:P220S	P	+	1	0	MAML1	179125275	1.000000	0.71417	0.968000	0.41197	0.839000	0.47603	7.442000	0.80503	2.251000	0.74343	0.455000	0.32223	CCT		0.517	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		5	46	5	46
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	32166813	32166813	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:32166813G>A	ENST00000375023.3	-	24	4563	c.4425C>T	c.(4423-4425)cgC>cgT	p.R1475R	NOTCH4_ENST00000443903.2_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1475	Poly-Arg.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CATGCTCTCGGCGTCGACGCC	0.677																																																0													55.0	69.0	64.0					6																	32166813		1508	2707	4215	SO:0001819	synonymous_variant	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4425C>T	6.37:g.32166813G>A			B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																				0.677	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			32	46	32	46
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu	37	6	32190325	32190325	+	Silent	SNP	C	C	T	rs201835213	byFrequency	TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:32190325C>T	ENST00000375023.3	-	3	552	c.414G>A	c.(412-414)tcG>tcA	p.S138S		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	138	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GTGGGCGGCCCGAGGCCTGGA	0.647													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18668	0.0		0.0	False		,,,				2504	0.001															0													29.0	32.0	31.0					6																	32190325		2195	4295	6490	SO:0001819	synonymous_variant	4855				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.414G>A	6.37:g.32190325C>T			B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																				0.647	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			8	69	8	69
PNPLA1	285848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	36262065	36262065	+	Silent	SNP	C	C	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:36262065C>A	ENST00000394571.2	+	4	603	c.603C>A	c.(601-603)ccC>ccA	p.P201P	PNPLA1_ENST00000388715.3_Silent_p.P106P|PNPLA1_ENST00000312917.5_Silent_p.P115P	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	201					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						ACATCTGTCCCCGGGACTGCC	0.607																																																0													100.0	79.0	86.0					6																	36262065		2203	4300	6503	SO:0001819	synonymous_variant	285848				CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.603C>A	6.37:g.36262065C>A			A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																				0.607	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		24	138	24	138
PPP2R5D	5528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	42974286	42974286	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:42974286C>T	ENST00000485511.1	+	3	370	c.191C>T	c.(190-192)cCg>cTg	p.P64L	PPP2R5D_ENST00000461010.1_Intron|PPP2R5D_ENST00000394110.3_Missense_Mutation_p.P64L|PPP2R5D_ENST00000472118.1_Missense_Mutation_p.P56L	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	64					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			AATAGCACGCCGCCCCCCACG	0.622																																					Melanoma(63;587 1613 29742 31770)											0													58.0	67.0	64.0					6																	42974286		2203	4300	6503	SO:0001583	missense	5528			L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9312	protein-coding gene	gene with protein product		601646	"""protein phosphatase 2, regulatory subunit B (B56), delta isoform"", ""protein phosphatase 2, regulatory subunit B', delta isoform"""			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.191C>T	6.37:g.42974286C>T	ENSP00000417963:p.Pro64Leu		A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Missense_Mutation	SNP	ENST00000485511.1	37	CCDS4878.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.844935	0.51164	.	.	ENSG00000112640	ENST00000485511;ENST00000394110;ENST00000472118;ENST00000541610	T;T;T	0.52983	0.73;0.86;0.64	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.55481	0.1923	M	0.80616	2.505	0.80722	D	1	P;D	0.71674	0.946;0.998	B;P	0.62491	0.436;0.903	T	0.56013	-0.8049	10	0.08599	T	0.76	-19.2065	17.4604	0.87619	0.0:1.0:0.0:0.0	.	64;64	Q14738;Q14738-2	2A5D_HUMAN;.	L	64;64;56;64	ENSP00000417963:P64L;ENSP00000377669:P64L;ENSP00000420550:P56L	ENSP00000377669:P64L	P	+	2	0	PPP2R5D	43082264	1.000000	0.71417	0.452000	0.26994	0.099000	0.18886	7.339000	0.79282	2.793000	0.96121	0.561000	0.74099	CCG		0.622	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245		76	130	76	130
TTBK1	84630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	43251409	43251409	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:43251409G>A	ENST00000259750.4	+	14	3014	c.2931G>A	c.(2929-2931)gcG>gcA	p.A977A		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	977					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GGGCCCGAGCGCCCCTGGAGA	0.697																																																0													21.0	26.0	24.0					6																	43251409		2200	4296	6496	SO:0001819	synonymous_variant	84630			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2931G>A	6.37:g.43251409G>A			A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																				0.697	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			26	32	26	32
ZNF292	23036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	87943087	87943087	+	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:87943087A>G	ENST00000369577.3	+	5	626	c.583A>G	c.(583-585)Aga>Gga	p.R195G	ZNF292_ENST00000339907.4_Missense_Mutation_p.R190G	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	195						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GTTGGATATGAGAATTAAACA	0.308																																																0													84.0	80.0	81.0					6																	87943087		1826	4078	5904	SO:0001583	missense	23036			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.583A>G	6.37:g.87943087A>G	ENSP00000358590:p.Arg195Gly		Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.439114	0.63067	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.37411	1.27;1.2	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	M	0.77313	2.365	0.43183	D	0.995001	D	0.89917	1.0	D	0.85130	0.997	T	0.58679	-0.7594	10	0.87932	D	0	.	11.2689	0.49127	0.7244:0.2756:0.0:0.0	.	195	O60281	ZN292_HUMAN	G	195;190	ENSP00000358590:R195G;ENSP00000342847:R190G	ENSP00000342847:R190G	R	+	1	2	ZNF292	87999806	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.309000	0.43699	2.158000	0.67659	0.460000	0.39030	AGA		0.308	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		9	22	9	22
RUNX1T1	862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	92972658	92972658	+	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr8:92972658C>G	ENST00000523629.1	-	12	2081	c.1627G>C	c.(1627-1629)Gac>Cac	p.D543H	RUNX1T1_ENST00000360348.2_Missense_Mutation_p.D506H|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.D506H|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.D516H|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.D543H|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.D516H|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.D506H|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.D554H	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	543					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TTCTCCCAGTCTTTGTGCTGG	0.567																																																0													90.0	79.0	83.0					8																	92972658		2203	4300	6503	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1627G>C	8.37:g.92972658C>G	ENSP00000428543:p.Asp543His		B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233862	0.79688	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.52057	0.68;0.74;0.68;0.76;0.76;0.76;0.71;0.74	5.86	5.86	0.93980	Zinc finger, MYND-type (3);	0.000000	0.85682	D	0.000000	T	0.60689	0.2288	L	0.28776	0.89	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;1.0;1.0;0.999	T	0.59968	-0.7354	10	0.52906	T	0.07	-24.1858	20.1802	0.98196	0.0:1.0:0.0:0.0	.	554;506;543;516	E7EPN4;Q7Z4J5;Q06455;Q06455-2	.;.;MTG8_HUMAN;.	H	543;516;543;506;506;506;554;516	ENSP00000428543:D543H;ENSP00000379520:D516H;ENSP00000265814:D543H;ENSP00000353504:D506H;ENSP00000390137:D506H;ENSP00000428742:D506H;ENSP00000402257:D554H;ENSP00000430728:D516H	ENSP00000265814:D543H	D	-	1	0	RUNX1T1	93041834	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.777000	0.95525	0.655000	0.94253	GAC		0.567	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		10	40	10	40
PLEC	5339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	144995732	144995732	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr8:144995732C>T	ENST00000322810.4	-	32	8837	c.8668G>A	c.(8668-8670)Gct>Act	p.A2890T	PLEC_ENST00000398774.2_Missense_Mutation_p.A2721T|PLEC_ENST00000356346.3_Missense_Mutation_p.A2739T|PLEC_ENST00000357649.2_Missense_Mutation_p.A2757T|PLEC_ENST00000345136.3_Missense_Mutation_p.A2753T|PLEC_ENST00000436759.2_Missense_Mutation_p.A2780T|PLEC_ENST00000354589.3_Missense_Mutation_p.A2753T|PLEC_ENST00000354958.2_Missense_Mutation_p.A2731T|PLEC_ENST00000527096.1_Missense_Mutation_p.A2776T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2890	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TCCTTCACAGCCTCGTTGACG	0.687																																																0													29.0	37.0	34.0					8																	144995732		2072	4189	6261	SO:0001583	missense	5339			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8668G>A	8.37:g.144995732C>T	ENSP00000323856:p.Ala2890Thr		Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.416390	0.25552	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	D;D;D;D;D;D;D;D;D	0.97598	-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45	4.44	4.44	0.53790	.	0.089485	0.42964	U	0.000629	D	0.98648	0.9547	H	0.95539	3.685	0.54753	D	0.999989	D;D;D;D;D;D;D;D	0.63880	0.992;0.992;0.992;0.993;0.992;0.992;0.992;0.992	P;P;P;P;P;P;P;P	0.58013	0.74;0.74;0.74;0.831;0.74;0.74;0.74;0.74	D	0.99421	1.0933	10	0.59425	D	0.04	.	17.2034	0.86912	0.0:1.0:0.0:0.0	.	2780;2739;2731;2890;2721;2753;2757;2753	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	T	2753;2757;2753;2721;2890;2731;2739;2780;2776	ENSP00000344848:A2753T;ENSP00000350277:A2757T;ENSP00000346602:A2753T;ENSP00000381756:A2721T;ENSP00000323856:A2890T;ENSP00000347044:A2731T;ENSP00000348702:A2739T;ENSP00000388180:A2780T;ENSP00000434583:A2776T	ENSP00000323856:A2890T	A	-	1	0	PLEC	145067720	1.000000	0.71417	0.958000	0.39756	0.210000	0.24377	4.539000	0.60657	2.470000	0.83445	0.442000	0.29010	GCT		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		30	44	30	44
GNE	10020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	36249251	36249251	+	Silent	SNP	G	G	A	rs147290887		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr9:36249251G>A	ENST00000539815.1	-	1	142	c.102C>T	c.(100-102)acC>acT	p.T34T	GNE_ENST00000539208.1_Intron|GNE_ENST00000396594.3_Silent_p.T65T|GNE_ENST00000543356.2_Intron|GNE_ENST00000377902.5_Silent_p.T34T|GNE_ENST00000447283.2_Silent_p.T34T			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	34					carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			ACTCAGGTTCGGTTTTAATGC	0.408																																					GBM(184;106 2118 20004 35750 50727)											0													175.0	146.0	156.0					9																	36249251		2203	4300	6503	SO:0001819	synonymous_variant	10020			AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"""UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"""	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.102C>T	9.37:g.36249251G>A			A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Silent	SNP	ENST00000539815.1	37	CCDS6602.1																																																																																				0.408	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		9	65	9	65
ALDH1A1	216	hgsc.bcm.edu;ucsc.edu	37	9	75520933	75520933	+	Silent	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr9:75520933G>A	ENST00000297785.3	-	12	1428	c.1374C>T	c.(1372-1374)ggC>ggT	p.G458G		NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	458					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	CACTTACCACGCCATAGCAAT	0.348																																																0													60.0	59.0	60.0					9																	75520933		2203	4300	6503	SO:0001819	synonymous_variant	216			K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.1374C>T	9.37:g.75520933G>A			O00768|Q5SYR1	Silent	SNP	ENST00000297785.3	37	CCDS6644.1																																																																																				0.348	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1			6	37	6	37
FPGS	2356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	130570869	130570869	+	Silent	SNP	C	C	G			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr9:130570869C>G	ENST00000373247.2	+	10	905	c.855C>G	c.(853-855)gcC>gcG	p.A285A	FPGS_ENST00000393706.2_Silent_p.A259A|FPGS_ENST00000373245.1_Intron|FPGS_ENST00000373225.3_Silent_p.A235A|FPGS_ENST00000460181.1_3'UTR	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	285					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	TGCTGGAGGCCCTCGAGGAAG	0.687																																																0													14.0	14.0	14.0					9																	130570869		2199	4297	6496	SO:0001819	synonymous_variant	2356				CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.855C>G	9.37:g.130570869C>G			B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Silent	SNP	ENST00000373247.2	37	CCDS35148.1																																																																																				0.687	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1			20	29	20	29
NOTCH1	4851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	139412597	139412597	+	Missense_Mutation	SNP	C	C	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr9:139412597C>A	ENST00000277541.6	-	7	1322	c.1247G>T	c.(1246-1248)tGc>tTc	p.C416F	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	416	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)			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)		ACCCAGCGAGCACTCATCCAC	0.672			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													42.0	45.0	44.0					9																	139412597		2019	4168	6187	SO:0001583	missense	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.1247G>T	9.37:g.139412597C>A	ENSP00000277541:p.Cys416Phe		Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413723	0.83449	.	.	ENSG00000148400	ENST00000277541	D	0.99445	-5.91	4.82	4.82	0.62117	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99809	0.9917	H	0.99770	4.765	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96455	0.9337	10	0.72032	D	0.01	.	16.8825	0.86067	0.0:1.0:0.0:0.0	.	416	P46531	NOTC1_HUMAN	F	416	ENSP00000277541:C416F	ENSP00000277541:C416F	C	-	2	0	NOTCH1	138532418	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	7.304000	0.78882	2.223000	0.72356	0.514000	0.50259	TGC		0.672	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		9	10	9	10
FTSJ1	24140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	48339829	48339829	+	Missense_Mutation	SNP	G	G	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chrX:48339829G>T	ENST00000348411.2	+	8	807	c.484G>T	c.(484-486)Gat>Tat	p.D162Y	FTSJ1_ENST00000396894.4_Missense_Mutation_p.D25Y|FTSJ1_ENST00000456787.1_Missense_Mutation_p.D162Y|FTSJ1_ENST00000496365.1_3'UTR|FTSJ1_ENST00000019019.2_Missense_Mutation_p.D162Y	NM_012280.2	NP_036412.1			FtsJ RNA methyltransferase homolog 1 (E. coli)											breast(1)|central_nervous_system(1)|lung(4)|skin(1)	7						CCGAGGCCGGGATGTGACGCT	0.602																																																0													71.0	63.0	66.0					X																	48339829		2203	4300	6503	SO:0001583	missense	24140			AJ005892	CCDS14294.1, CCDS14295.1, CCDS75972.1	Xp11.23	2012-06-12	2012-06-12		ENSG00000068438	ENSG00000068438			13254	protein-coding gene	gene with protein product	"""tRNA methyltransferase 7 homolog (S. cerevisiae)"""	300499	"""mental retardation, X-linked 9"", ""mental retardation, X-linked 44"""	MRX9, MRX44		15342698, 15162322	Standard	XR_246715		Approved	JM23, CDLIV, SPB1, TRM7, TRMT7	uc004djo.1	Q9UET6	OTTHUMG00000024118	ENST00000348411.2:c.484G>T	X.37:g.48339829G>T	ENSP00000326948:p.Asp162Tyr			Missense_Mutation	SNP	ENST00000348411.2	37	CCDS14294.1	.	.	.	.	.	.	.	.	.	.	g	16.12	3.031709	0.54790	.	.	ENSG00000068438	ENST00000019019;ENST00000348411;ENST00000396894;ENST00000456787	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	4.73	2.96	0.34315	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.110377	0.64402	D	0.000014	T	0.55081	0.1898	M	0.85299	2.745	0.46298	D	0.998977	D;D;B;P	0.89917	1.0;1.0;0.337;0.883	D;D;B;P	0.91635	0.999;0.996;0.43;0.566	T	0.56414	-0.7983	10	0.87932	D	0	-9.4554	8.5418	0.33397	0.1946:0.0:0.8054:0.0	.	25;162;162;162	B7Z4K4;Q9UET6;Q9UET6-2;B3KN91	.;RRMJ1_HUMAN;.;.	Y	162;162;25;162	ENSP00000019019:D162Y;ENSP00000326948:D162Y;ENSP00000380103:D25Y;ENSP00000415457:D162Y	ENSP00000019019:D162Y	D	+	1	0	FTSJ1	48224773	1.000000	0.71417	0.996000	0.52242	0.551000	0.35334	8.296000	0.89940	0.548000	0.28955	0.507000	0.49892	GAT		0.602	FTSJ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060726.1			30	11	30	11
LHFPL1	340596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	111914414	111914414	+	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chrX:111914414G>A	ENST00000371968.3	-	2	444	c.205C>T	c.(205-207)Cgc>Tgc	p.R69C	LHFPL1_ENST00000478229.1_Intron|LHFPL1_ENST00000536453.1_Missense_Mutation_p.R69C	NM_178175.3	NP_835469.1	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	69						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)	13						CTGGCATAGCGCCCACATTCT	0.592																																																0													141.0	125.0	130.0					X																	111914414		2203	4300	6503	SO:0001583	missense	340596			AY217350	CCDS14562.1	Xq23	2008-02-05			ENSG00000182508	ENSG00000182508			6587	protein-coding gene	gene with protein product		300566				10329012	Standard	NM_178175		Approved		uc004epq.3	Q86WI0	OTTHUMG00000022214	ENST00000371968.3:c.205C>T	X.37:g.111914414G>A	ENSP00000361036:p.Arg69Cys		A8K1N1|Q496M9|Q496N0|Q6UXU2	Missense_Mutation	SNP	ENST00000371968.3	37	CCDS14562.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.861972	0.71949	.	.	ENSG00000182508	ENST00000371968;ENST00000536453	T;T	0.73152	-0.72;-0.72	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.83166	0.5195	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.83944	0.0313	10	0.49607	T	0.09	-29.645	10.2057	0.43112	0.0:0.0:0.8026:0.1974	.	69;69	Q86WI0-2;Q86WI0	.;LHPL1_HUMAN	C	69	ENSP00000361036:R69C;ENSP00000444573:R69C	ENSP00000361036:R69C	R	-	1	0	LHFPL1	111801070	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.553000	0.53713	2.456000	0.83038	0.600000	0.82982	CGC		0.592	LHFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057947.1	NM_178175		36	69	36	69
NSDHL	50814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	152037637	152037637	+	Missense_Mutation	SNP	C	C	T	rs199567542		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chrX:152037637C>T	ENST00000370274.3	+	8	1293	c.1099C>T	c.(1099-1101)Cgc>Tgc	p.R367C	NSDHL_ENST00000440023.1_Missense_Mutation_p.R367C	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	367					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					GCAGAGCTTTCGCCACCTGCG	0.552													C|||	1	0.000264901	0.0008	0.0	3775	,	,		15084	0.0		0.0	False		,,,				2504	0.0															0													57.0	45.0	49.0					X																	152037637		2203	4300	6503	SO:0001583	missense	50814			X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	13398	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 31E, member 1"""	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.1099C>T	X.37:g.152037637C>T	ENSP00000359297:p.Arg367Cys		D3DWT6|O00344	Missense_Mutation	SNP	ENST00000370274.3	37	CCDS14717.1	1	6.027727546714888E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.451	1.090666	0.20471	.	.	ENSG00000147383	ENST00000370274;ENST00000440023	D;D	0.89485	-2.52;-2.52	4.3	3.42	0.39159	.	0.424993	0.27076	N	0.021057	T	0.82042	0.4951	L	0.47716	1.5	0.30541	N	0.766452	P	0.47841	0.901	B	0.40329	0.326	T	0.81106	-0.1083	10	0.54805	T	0.06	-21.716	4.92	0.13865	0.0:0.7493:0.0:0.2507	.	367	Q15738	NSDHL_HUMAN	C	367	ENSP00000359297:R367C;ENSP00000391854:R367C	ENSP00000359297:R367C	R	+	1	0	NSDHL	151788293	0.011000	0.17503	0.131000	0.22000	0.349000	0.29174	1.844000	0.39269	2.071000	0.62044	0.544000	0.68410	CGC		0.552	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922		11	29	11	29
ABI3BP	25890	broad.mit.edu;ucsc.edu	37	3	100523693	100523693	+	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr3:100523693G>A	ENST00000284322.5	-	20	1799	c.1690C>T	c.(1690-1692)Cgt>Tgt	p.R564C	ABI3BP_ENST00000471714.1_Missense_Mutation_p.R1241C|ABI3BP_ENST00000383691.4_Missense_Mutation_p.R518C	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	564	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						GCAGTAACACGCTGGGGCACC	0.398																																																0													182.0	170.0	174.0					3																	100523693		1916	4135	6051	SO:0001583	missense	25890			AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1690C>T	3.37:g.100523693G>A	ENSP00000284322:p.Arg564Cys		B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.98|12.98	2.100641|2.100641	0.37048|0.37048	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000466947|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000383691;ENST00000486770;ENST00000482765	.|T;T;T	.|0.56776	.|2.06;0.44;1.55	5.18|5.18	1.04|1.04	0.20106|0.20106	.|.	.|1.178940	.|0.05926	.|N	.|0.634394	T|T	0.59183|0.59183	0.2175|0.2175	L|L	0.49126|0.49126	1.545|1.545	0.09310|0.09310	N|N	1|1	.|D;D;D;D	.|0.89917	.|0.999;0.959;1.0;0.999	.|P;B;P;P	.|0.61722	.|0.719;0.416;0.893;0.719	T|T	0.43556|0.43556	-0.9384|-0.9384	5|10	.|0.46703	.|T	.|0.11	2.6408|2.6408	2.9177|2.9177	0.05759|0.05759	0.0897:0.1578:0.4278:0.3248|0.0897:0.1578:0.4278:0.3248	.|.	.|518;564;1241;248	.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.|.;TARSH_HUMAN;.;.	V|C	121|1241;564;248;518;2;113	.|ENSP00000420524:R1241C;ENSP00000284322:R564C;ENSP00000373189:R518C	.|ENSP00000284322:R564C	A|R	-|-	2|1	0|0	ABI3BP|ABI3BP	102006383|102006383	0.001000|0.001000	0.12720|0.12720	0.051000|0.051000	0.19133|0.19133	0.618000|0.618000	0.37518|0.37518	0.619000|0.619000	0.24388|0.24388	0.524000|0.524000	0.28502|0.28502	0.543000|0.543000	0.68304|0.68304	GCG|CGT		0.398	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			13	40	13	40
CRIP3	401262	broad.mit.edu;ucsc.edu	37	6	43275627	43275627	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr6:43275627C>T	ENST00000274990.4	-	3	150	c.146G>A	c.(145-147)gGg>gAg	p.G49E	CRIP3_ENST00000372569.3_Missense_Mutation_p.G49E|ZNF318_ENST00000607252.1_5'UTR			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	49	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			GTATGGCCTCCCATTGTGCTG	0.607																																																0													39.0	34.0	36.0					6																	43275627		2203	4300	6503	SO:0001583	missense	401262			AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.146G>A	6.37:g.43275627C>T	ENSP00000274990:p.Gly49Glu		A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	37		.	.	.	.	.	.	.	.	.	.	C	23.5	4.418347	0.83559	.	.	ENSG00000146215	ENST00000372569;ENST00000274990	D;D	0.88354	-2.37;-2.37	5.52	5.52	0.82312	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.93828	0.8026	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93522	0.6862	9	.	.	.	-44.6176	15.295	0.73898	0.0:1.0:0.0:0.0	.	49;49	Q6Q6R5;Q6Q6R5-3	CRIP3_HUMAN;.	E	49	ENSP00000361650:G49E;ENSP00000274990:G49E	.	G	-	2	0	CRIP3	43383605	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.742000	0.62103	2.748000	0.94277	0.655000	0.94253	GGG		0.607	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			4	35	4	35
KPRP	448834	broad.mit.edu;ucsc.edu	37	1	152733157	152733157	+	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr1:152733157G>A	ENST00000606109.1	+	1	1121	c.1093G>A	c.(1093-1095)Gcc>Acc	p.A365T	KPRP_ENST00000368773.1_Missense_Mutation_p.A365T			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	365	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.A365T(1)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTGGGGCGCCTCCTGCCC	0.662																																																1	Substitution - Missense(1)	prostate(1)											60.0	62.0	61.0					1																	152733157		2203	4300	6503	SO:0001583	missense	448834			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1093G>A	1.37:g.152733157G>A	ENSP00000475216:p.Ala365Thr			Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	0.479	-0.880953	0.02530	.	.	ENSG00000203786	ENST00000368773	T	0.11930	2.73	4.62	-6.99	0.01605	.	0.929655	0.09000	N	0.863063	T	0.00998	0.0033	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42716	-0.9435	10	0.05436	T	0.98	0.0126	6.3376	0.21304	0.496:0.0:0.3045:0.1995	.	365	Q5T749	KPRP_HUMAN	T	365	ENSP00000357762:A365T	ENSP00000357762:A365T	A	+	1	0	KPRP	150999781	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	-0.811000	0.04500	-2.255000	0.00696	-1.598000	0.00824	GCC		0.662	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		13	84	13	84
TTC12	54970	broad.mit.edu;ucsc.edu	37	11	113215006	113215006	+	Missense_Mutation	SNP	G	G	A	rs373487103		TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr11:113215006G>A	ENST00000529221.1	+	13	1103	c.998G>A	c.(997-999)cGt>cAt	p.R333H	TTC12_ENST00000478125.1_3'UTR|TTC12_ENST00000393020.1_Missense_Mutation_p.R333H|TTC12_ENST00000483239.2_Missense_Mutation_p.R339H|TTC12_ENST00000314756.3_Missense_Mutation_p.R333H	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	333										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		GAAAACCAGCGTGTGCTAGTG	0.532																																																0								G	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	143.0	115.0	124.0		998	3.5	1.0	11		124	1,8591	1.2+/-3.3	0,1,4295	no	missense	TTC12	NM_017868.3	29	0,2,6495	AA,AG,GG		0.0116,0.0227,0.0154	benign	333/706	113215006	2,12992	2201	4296	6497	SO:0001583	missense	54970			AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.998G>A	11.37:g.113215006G>A	ENSP00000433757:p.Arg333His		Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	CCDS8360.2	.	.	.	.	.	.	.	.	.	.	G	13.45	2.240578	0.39598	2.27E-4	1.16E-4	ENSG00000149292	ENST00000529221;ENST00000314756;ENST00000393020;ENST00000483239	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.41	3.55	0.40652	Armadillo-like helical (1);Armadillo-type fold (1);	1.159190	0.06105	N	0.666071	T	0.46092	0.1375	M	0.62723	1.935	0.42406	D	0.992585	B;B	0.28605	0.217;0.217	B;B	0.19148	0.024;0.024	T	0.38802	-0.9644	10	0.51188	T	0.08	-14.8881	9.0705	0.36488	0.1709:0.0:0.8291:0.0	.	333;333	A8K8G6;Q9H892	.;TTC12_HUMAN	H	333;333;333;339	ENSP00000433757:R333H;ENSP00000315160:R333H;ENSP00000376743:R333H;ENSP00000419652:R339H	ENSP00000315160:R333H	R	+	2	0	TTC12	112720216	0.980000	0.34600	0.996000	0.52242	0.844000	0.47949	1.217000	0.32455	1.285000	0.44548	-0.126000	0.14955	CGT		0.532	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868		73	126	73	126
THSD7B	80731	broad.mit.edu;ucsc.edu	37	2	137814593	137814593	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr2:137814593G>A	ENST00000409968.1	+	3	921	c.743G>A	c.(742-744)tGg>tAg	p.W248*	THSD7B_ENST00000272643.3_Nonsense_Mutation_p.W248*|THSD7B_ENST00000543459.1_Nonsense_Mutation_p.W107*|THSD7B_ENST00000413152.2_Nonsense_Mutation_p.W217*			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	248						integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		GTTGGACCATGGAGTAAATGC	0.413																																																0													154.0	151.0	152.0					2																	137814593		1885	4119	6004	SO:0001587	stop_gained	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.743G>A	2.37:g.137814593G>A	ENSP00000387145:p.Trp248*			Nonsense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.575845	0.96553	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152;ENST00000543459	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.2348	0.93855	0.0:0.0:1.0:0.0	.	.	.	.	X	248;248;217;107	.	ENSP00000272643:W248X	W	+	2	0	THSD7B	137531063	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.813000	0.99286	2.721000	0.93114	0.585000	0.79938	TGG		0.413	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		39	59	39	59
DIXDC1	85458	broad.mit.edu;ucsc.edu	37	11	111835363	111835363	+	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr11:111835363C>T	ENST00000529225.1	+	3	428	c.148C>T	c.(148-150)Cgg>Tgg	p.R50W	DIXDC1_ENST00000531396.1_Missense_Mutation_p.R51W|DIXDC1_ENST00000389821.4_3'UTR|DIXDC1_ENST00000440460.2_Missense_Mutation_p.R51W	NM_001278542.1	NP_001265471.1	Q155Q3	DIXC1_HUMAN	DIX domain containing 1	51	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				camera-type eye development (GO:0043010)|cell cycle (GO:0007049)|cerebellar cortex development (GO:0021695)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain development (GO:0030900)|forebrain ventricular zone progenitor cell division (GO:0021869)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of axonogenesis (GO:0050772)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JNK cascade (GO:0046330)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of JNK cascade (GO:0046328)|regulation of microtubule cytoskeleton organization (GO:0070507)|Wnt signaling pathway (GO:0016055)	axon terminus (GO:0043679)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytosol (GO:0005829)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	gamma-tubulin binding (GO:0043015)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)			cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		ACAAGATCTCCGGGATGGGGT	0.517																																																0													65.0	69.0	68.0					11																	111835363		1957	4149	6106	SO:0001583	missense	85458			AB051522	CCDS60957.1, CCDS73381.1, CCDS73382.1	11q23.1	2014-03-20			ENSG00000150764	ENSG00000150764			23695	protein-coding gene	gene with protein product		610493				12792787	Standard	NM_001037954		Approved	KIAA1735, Dixin	uc001pmm.3	Q155Q3	OTTHUMG00000166912	ENST00000529225.1:c.148C>T	11.37:g.111835363C>T	ENSP00000434130:p.Arg50Trp		A1A5D8|E9PRV4|Q6P2J8|Q6PIK4|Q86SR7|Q8IVY4|Q96N69|Q9C0C8	Missense_Mutation	SNP	ENST00000529225.1	37		.	.	.	.	.	.	.	.	.	.	C	21.6	4.174128	0.78452	.	.	ENSG00000150764	ENST00000529225;ENST00000440460;ENST00000531396	T;T;T	0.62232	0.04;0.04;0.04	4.96	4.96	0.65561	Calponin homology domain (5);	0.000000	0.49916	D	0.000127	T	0.80232	0.4585	M	0.82716	2.605	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.984;0.987	T	0.83111	-0.0123	10	0.87932	D	0	-20.0946	14.8726	0.70471	0.1437:0.8563:0.0:0.0	.	51;51;50	Q155Q3;Q155Q3-4;E9PRV4	DIXC1_HUMAN;.;.	W	50;51;51	ENSP00000434130:R50W;ENSP00000394352:R51W;ENSP00000432959:R51W	ENSP00000394352:R51W	R	+	1	2	DIXDC1	111340573	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.394000	0.59671	2.590000	0.87494	0.467000	0.42956	CGG		0.517	DIXDC1-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000391831.1	NM_001037954		7	9	7	9
HFM1	164045	broad.mit.edu;hgsc.bcm.edu	37	1	91781979	91781980	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr1:91781979_91781980insT	ENST00000370425.3	-	26	2964_2965	c.2866_2867insA	c.(2866-2868)atafs	p.I956fs	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Frame_Shift_Ins_p.I188fs|HFM1_ENST00000370424.3_Frame_Shift_Ins_p.I635fs	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	956	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGTCTCTTCTATTTTTTTAAAG	0.292																																																0																																										SO:0001589	frameshift_variant	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2867dupA	1.37:g.91781986_91781986dupT	ENSP00000359454:p.Ile956fs		B1B0B6|Q8N9Q0	Frame_Shift_Ins	INS	ENST00000370425.3	37	CCDS30769.2																																																																																				0.292	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		29	20	29	20
KIAA1147	57189	broad.mit.edu;hgsc.bcm.edu	37	7	141362626	141362626	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr7:141362626delT	ENST00000536163.1	-	9	1197	c.1198delA	c.(1198-1200)atafs	p.I400fs	RP5-894A10.6_ENST00000602609.1_RNA|KIAA1147_ENST00000482493.1_Frame_Shift_Del_p.I296fs	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	400										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					GTCTGAAATATCCGGTTGTTT	0.502																																																0													31.0	31.0	31.0					7																	141362626		1850	4090	5940	SO:0001589	frameshift_variant	57189			AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1198delA	7.37:g.141362626delT	ENSP00000445768:p.Ile400fs		Q9ULS3	Frame_Shift_Del	DEL	ENST00000536163.1	37	CCDS47726.1																																																																																				0.502	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			10	2	10	2
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42797750	42797750	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IK-8125-01A-11D-2253-08	TCGA-IK-8125-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1a94ffa8-b014-46c2-b0fc-e2ec18aa0d03	572ef2b3-0fb8-450b-9850-765fa3c1e051	g.chr19:42797750delA	ENST00000575354.2	+	16	3842	c.3802delA	c.(3802-3804)aaafs	p.K1268fs	CIC_ENST00000572681.2_Frame_Shift_Del_p.K2175fs|CIC_ENST00000160740.3_Frame_Shift_Del_p.K1266fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1268	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCAGGCCAGCAAATTCCCCAG	0.637			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													28.0	32.0	31.0					19																	42797750		2202	4299	6501	SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3802delA	19.37:g.42797750delA	ENSP00000458663:p.Lys1268fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.637	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			25	21	25	21
