#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
CDH23	64072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	73453969	73453969	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr10:73453969G>A	ENST00000224721.6	+	20	2262	c.2257G>A	c.(2257-2259)Gca>Aca	p.A753T	CDH23_ENST00000299366.7_Missense_Mutation_p.A793T	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	748	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CATCGTTCGCGCAGTGGACGG	0.627																																																0													66.0	82.0	77.0					10																	73453969		2081	4202	6283	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2257G>A	10.37:g.73453969G>A	ENSP00000224721:p.Ala753Thr		C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	G	27.3	4.822041	0.90873	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.068139	0.56097	N	0.000021	D	0.91085	0.7194	H	0.98559	4.265	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.977	D	0.94246	0.7489	9	0.87932	D	0	.	19.5163	0.95167	0.0:0.0:1.0:0.0	.	748;751;748	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	T	753;748;748;751;751;265	.	ENSP00000224721:A753T	A	+	1	0	CDH23	73123975	1.000000	0.71417	0.388000	0.26195	0.281000	0.26958	9.827000	0.99397	2.621000	0.88768	0.643000	0.83706	GCA		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		11	47	11	47
RELT	84957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	73102213	73102213	+	Silent	SNP	C	C	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr11:73102213C>T	ENST00000064780.2	+	5	573	c.312C>T	c.(310-312)ccC>ccT	p.P104P	RELT_ENST00000393580.2_Silent_p.P104P	NM_152222.1	NP_689408.1	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor	104						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	12						GGGGGGTTCCCCGCGTTCCAT	0.587																																																0													155.0	141.0	146.0					11																	73102213		2200	4293	6493	SO:0001819	synonymous_variant	84957			AF319553	CCDS8222.1	11q13.2	2013-05-22	2007-06-14	2007-06-14		ENSG00000054967		"""Tumor necrosis factor receptor superfamily"""	13764	protein-coding gene	gene with protein product		611211	"""tumor necrosis factor receptor superfamily, member 19-like"""	TNFRSF19L		11313261, 16547002, 16950202, 16389068	Standard	NM_032871		Approved	FLJ14993	uc001otv.3	Q969Z4		ENST00000064780.2:c.312C>T	11.37:g.73102213C>T			Q86V34|Q96JU1|Q9BUX7	Silent	SNP	ENST00000064780.2	37	CCDS8222.1																																																																																				0.587	RELT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397380.2	NM_032871		68	110	68	110
SYTL2	54843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	85420400	85420400	+	Silent	SNP	C	C	T	rs202024537		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr11:85420400C>T	ENST00000528231.1	-	12	2251	c.1974G>A	c.(1972-1974)gcG>gcA	p.A658A	SYTL2_ENST00000525423.1_Silent_p.A980A|SYTL2_ENST00000389960.4_Silent_p.A634A|SYTL2_ENST00000359152.5_Silent_p.A1504A|SYTL2_ENST00000527523.1_Silent_p.A626A|SYTL2_ENST00000533892.1_Silent_p.A60A|SYTL2_ENST00000354566.3_Silent_p.A996A|SYTL2_ENST00000524452.1_Silent_p.A634A|SYTL2_ENST00000389958.3_Silent_p.A89A|SYTL2_ENST00000525702.1_Silent_p.A100A|SYTL2_ENST00000316356.4_Silent_p.A659A|SYTL2_ENST00000529581.1_Silent_p.A100A	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	658	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.			A -> V (in Ref. 4; BAD18516). {ECO:0000305}.	exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTTTTACATCCGCTGCTGCTA	0.398													C|||	1	0.000199681	0.0	0.0	5008	,	,		17199	0.001		0.0	False		,,,				2504	0.0															0													128.0	128.0	128.0					11																	85420400		2203	4299	6502	SO:0001819	synonymous_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1974G>A	11.37:g.85420400C>T			B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																				0.398	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		49	141	49	141
CD3D	915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	118211223	118211223	+	Silent	SNP	C	C	T	rs201021372		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr11:118211223C>T	ENST00000300692.4	-	2	277	c.141G>A	c.(139-141)acG>acA	p.T47T	CD3D_ENST00000392884.2_Silent_p.T47T|CD3D_ENST00000529594.1_Intron	NM_000732.4	NP_000723.1	P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	47					cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	GTGTTCCCACCGTTCCCTCTA	0.458																																																0													196.0	146.0	163.0					11																	118211223		2200	4296	6496	SO:0001819	synonymous_variant	915			X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286		"""CD molecules"""	1673	protein-coding gene	gene with protein product		186790	"""CD3d antigen, delta polypeptide (TiT3 complex)"""	T3D			Standard	NM_000732		Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000300692.4:c.141G>A	11.37:g.118211223C>T			A8MVP6	Silent	SNP	ENST00000300692.4	37	CCDS8394.1	.	.	.	.	.	.	.	.	.	.	C	4.050	0.006917	0.07866	.	.	ENSG00000167286	ENST00000534687	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.35799	0.0944	.	.	.	0.36377	D	0.861673	.	.	.	.	.	.	T	0.52268	-0.8598	4	.	.	.	-10.8905	4.6572	0.12624	0.1415:0.0893:0.2231:0.5461	.	.	.	.	S	52	.	.	G	-	1	0	CD3D	117716433	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-4.212000	0.00273	-4.469000	0.00047	-1.020000	0.02445	GGT		0.458	CD3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392128.1	NM_000732		20	51	20	51
C11orf63	79864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	122774732	122774732	+	Silent	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr11:122774732G>A	ENST00000531316.1	+	2	536	c.444G>A	c.(442-444)ccG>ccA	p.P148P	C11orf63_ENST00000227349.2_Silent_p.P148P|C11orf63_ENST00000307257.6_Silent_p.P148P			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	148					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		AAGCGTTGCCGGAGTCCACGG	0.532																																																0													93.0	104.0	100.0					11																	122774732		2202	4299	6501	SO:0001819	synonymous_variant	0			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.444G>A	11.37:g.122774732G>A			A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	ENST00000531316.1	37	CCDS8438.1																																																																																				0.532	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		63	120	63	120
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	59272814	59272814	+	Silent	SNP	A	A	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr12:59272814A>C	ENST00000320743.3	-	14	2161	c.1875T>G	c.(1873-1875)gcT>gcG	p.A625A	LRIG3_ENST00000379141.4_Silent_p.A565A	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	625	Ig-like C2-type 2.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GCCCCACAGCAGCACACTCCA	0.587			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0													53.0	44.0	47.0					12																	59272814		2203	4300	6503	SO:0001819	synonymous_variant	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1875T>G	12.37:g.59272814A>C			Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																				0.587	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		13	40	13	40
COQ5	84274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	120966932	120966932	+	Missense_Mutation	SNP	C	C	A	rs527630225		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr12:120966932C>A	ENST00000288532.6	-	1	53	c.13G>T	c.(13-15)Ggg>Tgg	p.G5W	COQ5_ENST00000445328.2_Missense_Mutation_p.G5W	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	5					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCACAGCTCCCGGGGGCCGCC	0.652																																																0													14.0	16.0	15.0					12																	120966932		2200	4295	6495	SO:0001583	missense	84274			AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"""2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"""		"""coenzyme Q5 homolog, methyltransferase (yeast)"""				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.13G>T	12.37:g.120966932C>A	ENSP00000288532:p.Gly5Trp		B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Missense_Mutation	SNP	ENST00000288532.6	37	CCDS31912.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562498	0.45694	.	.	ENSG00000110871	ENST00000288532;ENST00000302223;ENST00000445328;ENST00000547943	T;T;T	0.76968	-0.06;-1.06;-0.06	5.9	-1.98	0.07480	.	1.262750	0.04611	N	0.400213	T	0.57621	0.2066	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48375	-0.9041	10	0.59425	D	0.04	.	5.8022	0.18420	0.1245:0.3647:0.0:0.5108	.	5;5	B4DP72;Q5HYK3	.;COQ5_HUMAN	W	5	ENSP00000288532:G5W;ENSP00000401798:G5W;ENSP00000449874:G5W	ENSP00000288532:G5W	G	-	1	0	COQ5	119451315	0.044000	0.20184	0.027000	0.17364	0.005000	0.04900	-0.140000	0.10342	-0.339000	0.08401	-0.294000	0.09567	GGG		0.652	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314		15	33	15	33
ABCC12	94160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	48162529	48162529	+	Silent	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr16:48162529G>A	ENST00000311303.3	-	9	1701	c.1356C>T	c.(1354-1356)acC>acT	p.T452T	ABCC12_ENST00000448542.1_Silent_p.T452T|ABCC12_ENST00000416054.1_Silent_p.T452T	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	452						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				ATTTCTTTGGGGTACTTTTCC	0.507																																																0													166.0	142.0	150.0					16																	48162529		2201	4300	6501	SO:0001819	synonymous_variant	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1356C>T	16.37:g.48162529G>A			Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																				0.507	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		33	66	33	66
MMP15	4324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	58072238	58072238	+	Missense_Mutation	SNP	G	G	A	rs147283654		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr16:58072238G>A	ENST00000219271.3	+	3	1165	c.380G>A	c.(379-381)cGg>cAg	p.R127Q		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	127					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	AACCTGCGGCGGCGTCGGAAG	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		20008	0.0		0.0	False		,,,				2504	0.001															0								G	GLN/ARG	0,4396		0,0,2198	102.0	96.0	98.0		380	3.1	1.0	16	dbSNP_134	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	MMP15	NM_002428.2	43	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	127/670	58072238	1,12995	2198	4300	6498	SO:0001583	missense	4324			Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"""matrix metalloproteinase 15 (membrane-inserted)"""			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.380G>A	16.37:g.58072238G>A	ENSP00000219271:p.Arg127Gln		A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.646111	0.67358	0.0	1.16E-4	ENSG00000102996	ENST00000219271	T	0.17213	2.29	4.22	3.11	0.35812	Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.22936	0.0554	L	0.38175	1.15	0.49299	D	0.999776	D	0.69078	0.997	D	0.67725	0.953	T	0.03017	-1.1082	10	0.12430	T	0.62	.	8.9742	0.35926	0.0:0.0:0.5688:0.4312	.	127	P51511	MMP15_HUMAN	Q	127	ENSP00000219271:R127Q	ENSP00000219271:R127Q	R	+	2	0	MMP15	56629739	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.416000	0.52707	2.096000	0.63516	0.462000	0.41574	CGG		0.647	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		57	158	57	158
PSKH1	5681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	67961376	67961376	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr16:67961376G>A	ENST00000291041.5	+	3	1276	c.1106G>A	c.(1105-1107)cGc>cAc	p.R369H		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	369						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		AACCTGCACCGCTCCATATCC	0.607																																																0													99.0	86.0	91.0					16																	67961376		2198	4300	6498	SO:0001583	missense	5681			M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.1106G>A	16.37:g.67961376G>A	ENSP00000291041:p.Arg369His		Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	37	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	36	5.913319	0.97099	.	.	ENSG00000159792	ENST00000291041	T	0.39592	1.07	5.19	5.19	0.71726	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.59985	0.2234	M	0.70275	2.135	0.80722	D	1	D	0.63046	0.992	P	0.56474	0.799	T	0.62651	-0.6809	10	0.54805	T	0.06	-11.2996	18.688	0.91573	0.0:0.0:1.0:0.0	.	369	P11801	KPSH1_HUMAN	H	369	ENSP00000291041:R369H	ENSP00000291041:R369H	R	+	2	0	PSKH1	66518877	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.578000	0.87016	0.655000	0.94253	CGC		0.607	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742		50	91	50	91
SLC44A5	204962	hgsc.bcm.edu;ucsc.edu	37	1	75716928	75716928	+	Silent	SNP	G	G	A	rs114123196	byFrequency	TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr1:75716928G>A	ENST00000370855.5	-	7	425	c.312C>T	c.(310-312)tcC>tcT	p.S104S	SLC44A5_ENST00000535611.1_5'UTR|SLC44A5_ENST00000370859.3_Silent_p.S104S|SLC44A5_ENST00000469525.1_5'UTR	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	104					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TTAGCAACACGGAGGGACTGG	0.413													G|||	25	0.00499201	0.0166	0.0029	5008	,	,		17686	0.0		0.0	False		,,,				2504	0.001															0								G	,	81,4325	69.8+/-107.6	0,81,2122	121.0	106.0	111.0		312,312	-9.6	0.0	1	dbSNP_132	111	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	0,81,6422	AA,AG,GG		0.0,1.8384,0.6228	,	104/718,104/720	75716928	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	204962			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.312C>T	1.37:g.75716928G>A			B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																				0.413	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697		31	73	31	73
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78432577	78432577	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr1:78432577T>C	ENST00000370768.2	-	6	487	c.406A>G	c.(406-408)Ata>Gta	p.I136V	FUBP1_ENST00000436586.2_Missense_Mutation_p.I157V|FUBP1_ENST00000370767.1_Missense_Mutation_p.I136V	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	136	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CCAGGAGCTATCTGTATTTTG	0.318			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													65.0	63.0	64.0					1																	78432577		2203	4299	6502	SO:0001583	missense	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.406A>G	1.37:g.78432577T>C	ENSP00000359804:p.Ile136Val		Q12828	Missense_Mutation	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.290193	0.80914	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.46	5.46	0.80206	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	N	0.25060	0.705	0.58432	D	0.999998	P;B	0.44946	0.846;0.374	P;B	0.51806	0.68;0.267	T	0.03287	-1.1052	10	0.23302	T	0.38	-12.2137	15.817	0.78612	0.0:0.0:0.0:1.0	.	157;136	B4DT31;Q96AE4	.;FUBP1_HUMAN	V	135;136;136;135;157;156	ENSP00000359803:I136V;ENSP00000359804:I136V;ENSP00000389536:I157V;ENSP00000402630:I156V	ENSP00000294623:I135V	I	-	1	0	FUBP1	78205165	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.191000	0.72063	2.193000	0.70182	0.533000	0.62120	ATA		0.318	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		21	26	21	26
MARK1	4139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	220791711	220791711	+	Silent	SNP	T	T	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr1:220791711T>C	ENST00000366917.4	+	8	878	c.612T>C	c.(610-612)agT>agC	p.S204S	MARK1_ENST00000402574.1_Silent_p.S69S|MARK1_ENST00000366918.4_Silent_p.S182S					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		TTGGTTTTAGTAATGAATTTA	0.383																																																0													51.0	55.0	54.0					1																	220791711		2203	4300	6503	SO:0001819	synonymous_variant	4139			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.612T>C	1.37:g.220791711T>C				Silent	SNP	ENST00000366917.4	37	CCDS31029.2																																																																																				0.383	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1			25	66	25	66
SSTR3	6753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	37603800	37603800	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr22:37603800G>T	ENST00000328544.3	-	2	576	c.43C>A	c.(43-45)Cct>Act	p.P15T	SSTR3_ENST00000402501.1_Missense_Mutation_p.P15T	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	15					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GCATTCTCAGGTTCTGAGGTC	0.632																																																0													58.0	55.0	56.0					22																	37603800		2203	4300	6503	SO:0001583	missense	6753				CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.43C>A	22.37:g.37603800G>T	ENSP00000330138:p.Pro15Thr		A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	G	0.709	-0.787734	0.02884	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.71698	-0.59;-0.59	5.61	2.31	0.28768	.	0.000000	0.85682	D	0.000000	T	0.54143	0.1840	L	0.47716	1.5	0.09310	N	0.999999	P	0.43094	0.799	B	0.33339	0.162	T	0.43360	-0.9396	10	0.22109	T	0.4	.	9.2642	0.37630	0.0802:0.4572:0.4626:0.0	.	15	P32745	SSR3_HUMAN	T	15	ENSP00000330138:P15T;ENSP00000384904:P15T	ENSP00000330138:P15T	P	-	1	0	SSTR3	35933746	0.522000	0.26266	0.016000	0.15963	0.018000	0.09664	1.743000	0.38258	0.292000	0.22492	0.557000	0.71058	CCT		0.632	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			22	53	22	53
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	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			32	56	32	56
MYH15	22989	hgsc.bcm.edu;broad.mit.edu	37	3	108172944	108172944	+	Missense_Mutation	SNP	C	C	G			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr3:108172944C>G	ENST00000273353.3	-	22	2424	c.2368G>C	c.(2368-2370)Gat>Cat	p.D790H	MYH15_ENST00000495753.2_5'Flank	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	790	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AGTCTCTCATCTCTTATTGCT	0.393																																																0													106.0	97.0	100.0					3																	108172944		1866	4111	5977	SO:0001583	missense	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2368G>C	3.37:g.108172944C>G	ENSP00000273353:p.Asp790His			Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.921934	0.52653	.	.	ENSG00000144821	ENST00000273353	T	0.72282	-0.64	5.25	0.586	0.17434	Myosin head, motor domain (1);	.	.	.	.	T	0.78641	0.4315	H	0.94964	3.605	0.47183	D	0.999345	P	0.42961	0.795	P	0.45998	0.5	T	0.76971	-0.2761	9	0.72032	D	0.01	.	7.141	0.25556	0.0:0.5851:0.2426:0.1723	.	790	Q9Y2K3	MYH15_HUMAN	H	790	ENSP00000273353:D790H	ENSP00000273353:D790H	D	-	1	0	MYH15	109655634	1.000000	0.71417	0.001000	0.08648	0.691000	0.40173	2.851000	0.48302	-0.112000	0.11979	0.655000	0.94253	GAT		0.393	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		5	55	5	55
YTHDC1	91746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	69179953	69179953	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr4:69179953C>T	ENST00000344157.4	-	17	2383	c.2048G>A	c.(2047-2049)cGg>cAg	p.R683Q	YTHDC1_ENST00000355665.3_Missense_Mutation_p.R665Q|YTHDC1_ENST00000579690.1_Missense_Mutation_p.R691Q	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	683	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						ctctcgttcccggtctctttc	0.493																																																0													87.0	75.0	79.0					4																	69179953		2203	4300	6503	SO:0001583	missense	91746			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.2048G>A	4.37:g.69179953C>T	ENSP00000339245:p.Arg683Gln		Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096850	0.76870	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.32988	1.44;1.43	5.41	5.41	0.78517	.	0.054973	0.64402	D	0.000001	T	0.34250	0.0891	L	0.29908	0.895	0.58432	D	0.999999	D;D	0.69078	0.997;0.995	P;P	0.51079	0.658;0.457	T	0.02070	-1.1219	10	0.27082	T	0.32	.	18.8065	0.92040	0.0:1.0:0.0:0.0	.	665;683	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	Q	683;665	ENSP00000339245:R683Q;ENSP00000347888:R665Q	ENSP00000339245:R683Q	R	-	2	0	YTHDC1	68862548	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.830000	0.75319	2.543000	0.85770	0.467000	0.42956	CGG		0.493	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		15	22	15	22
TENM2	57451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	167674845	167674845	+	Missense_Mutation	SNP	C	C	T	rs367824725		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr5:167674845C>T	ENST00000518659.1	+	27	6940	c.6901C>T	c.(6901-6903)Cgc>Tgc	p.R2301C	TENM2_ENST00000403607.2_Missense_Mutation_p.R2125C|TENM2_ENST00000520394.1_Missense_Mutation_p.R2062C|TENM2_ENST00000545108.1_Missense_Mutation_p.R2300C|TENM2_ENST00000519204.1_Missense_Mutation_p.R2180C	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2301					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGTCCAGTACCGCTATGATGG	0.567																																																0								C	CYS/ARG	1,4103		0,1,2051	98.0	100.0	99.0		6874	3.6	1.0	5		99	1,8377		0,1,4188	no	missense	ODZ2	NM_001122679.1	180	0,2,6239	TT,TC,CC		0.0119,0.0244,0.016	probably-damaging	2292/2766	167674845	2,12480	2052	4189	6241	SO:0001583	missense	57451			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6901C>T	5.37:g.167674845C>T	ENSP00000429430:p.Arg2301Cys		Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	16.04	3.009032	0.54361	2.44E-4	1.19E-4	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89939	-2.12;-2.11;-2.22;-2.57;-2.59	5.44	3.58	0.41010	.	0.047100	0.85682	D	0.000000	D	0.92071	0.7487	L	0.53249	1.67	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.72982	0.979;0.953;0.862	D	0.91321	0.5082	10	0.39692	T	0.17	.	14.6172	0.68558	0.2651:0.7349:0.0:0.0	.	2300;2301;2062	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	C	2301;2300;2180;2062;2125	ENSP00000429430:R2301C;ENSP00000438635:R2300C;ENSP00000428964:R2180C;ENSP00000427874:R2062C;ENSP00000384905:R2125C	ENSP00000384905:R2125C	R	+	1	0	ODZ2	167607423	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.936000	0.63506	1.280000	0.44463	0.561000	0.74099	CGC		0.567	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		38	118	38	118
BTNL3	10917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	180420089	180420089	+	Missense_Mutation	SNP	T	T	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr5:180420089T>A	ENST00000342868.6	+	2	510	c.326T>A	c.(325-327)aTc>aAc	p.I109N		NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	109						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			CCCTCGGACATCGGCCTGTAT	0.522																																																0													74.0	70.0	72.0					5																	180420089		1962	3790	5752	SO:0001583	missense	10917			AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.326T>A	5.37:g.180420089T>A	ENSP00000341787:p.Ile109Asn		Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	37	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	T	7.686	0.690055	0.15039	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.64260	-0.09	2.9	-5.8	0.02347	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.18841	0.0452	N	0.00483	-1.445	0.09310	N	1	B	0.30889	0.299	B	0.26310	0.068	T	0.32322	-0.9911	9	0.06494	T	0.89	.	7.8936	0.29693	0.7293:0.1625:0.0:0.1082	.	109	Q6UXE8	BTNL3_HUMAN	N	109	ENSP00000341787:I109N	ENSP00000341787:I109N	I	+	2	0	BTNL3	180352695	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.055000	0.11807	-1.114000	0.02977	-0.744000	0.03518	ATC		0.522	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975		13	2	13	2
SYNGAP1	8831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	33405883	33405883	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr6:33405883C>T	ENST00000418600.2	+	8	1302	c.1201C>T	c.(1201-1203)Cgg>Tgg	p.R401W	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.R401W|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R342W|MIR5004_ENST00000579078.1_RNA	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	401					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CCCGGCTGTGCGGCTGAAAGC	0.592																																																0													99.0	105.0	103.0					6																	33405883		2202	4299	6501	SO:0001583	missense	8831			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1201C>T	6.37:g.33405883C>T	ENSP00000403636:p.Arg401Trp		A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357316	0.61293	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	D;D;D	0.81659	-1.52;-1.52;-1.52	4.68	0.62	0.17637	Ras GTPase-activating protein (1);	0.000000	0.64402	D	0.000001	D	0.82522	0.5055	M	0.78916	2.43	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.993;0.997;0.997;1.0	T	0.81373	-0.0962	10	0.87932	D	0	.	7.0403	0.25017	0.4142:0.5022:0.0:0.0835	.	401;401;401;401	Q96PV0;Q96PV0-2;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.;.	W	401;401;401;342	ENSP00000293748:R401W;ENSP00000403636:R401W;ENSP00000412475:R342W	ENSP00000293748:R401W	R	+	1	2	SYNGAP1	33513861	0.997000	0.39634	0.923000	0.36655	0.955000	0.61496	3.140000	0.50585	-0.088000	0.12506	0.650000	0.86243	CGG		0.592	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		24	186	24	186
UQCC2	84300	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	33665498	33665498	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr6:33665498T>C	ENST00000607484.1	-	4	353	c.313A>G	c.(313-315)Aaa>Gaa	p.K105E	SBP1_ENST00000594414.1_5'Flank|MIR3934_ENST00000579806.1_RNA|UQCC2_ENST00000374214.3_Missense_Mutation_p.K80E	NM_032340.3	NP_115716.1	Q9BRT2	UQCC2_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 2	105					regulation of insulin secretion (GO:0050796)|regulation of oxidative phosphorylation (GO:0002082)|regulation of skeletal muscle cell differentiation (GO:2001014)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CACATGCCTTTATCTATTTCC	0.478																																																0													112.0	106.0	108.0					6																	33665498		2203	4300	6503	SO:0001583	missense	84300				CCDS4784.1	6p21.31	2013-09-20	2013-09-20	2013-09-20	ENSG00000137288	ENSG00000137288		"""Mitochondrial respiratory chain complex assembly factors"""	21237	protein-coding gene	gene with protein product	"""cytochrome B protein synthesis 6 homolog (S. cerevisiae)"""	614461	"""chromosome 6 open reading frame 125"", ""mitochondrial nucleoid factor 1"""	C6orf125, MNF1		19643811	Standard	NM_032340		Approved	MGC14833, bA6B20.2, M19, Cbp6	uc003ofa.2	Q9BRT2	OTTHUMG00000014534	ENST00000607484.1:c.313A>G	6.37:g.33665498T>C	ENSP00000476140:p.Lys105Glu		B2R4I0	Missense_Mutation	SNP	ENST00000607484.1	37	CCDS4784.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.174090	0.57692	.	.	ENSG00000137288	ENST00000374231;ENST00000374214	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	M	0.62209	1.925	0.42313	D	0.992225	D	0.65815	0.995	D	0.68765	0.96	T	0.72530	-0.4265	9	0.52906	T	0.07	.	14.0846	0.64947	0.0:0.0:0.0:1.0	.	105	Q9BRT2	CF125_HUMAN	E	105;80	.	ENSP00000363331:K80E	K	-	1	0	C6orf125	33773476	1.000000	0.71417	0.929000	0.37066	0.081000	0.17604	5.316000	0.65815	2.269000	0.75478	0.533000	0.62120	AAA		0.478	UQCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040207.2	NM_032340		28	63	28	63
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	152831491	152831491	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr6:152831491T>C	ENST00000367255.5	-	8	1019	c.418A>G	c.(418-420)Agc>Ggc	p.S140G	SYNE1_ENST00000367253.4_Missense_Mutation_p.S140G|SYNE1_ENST00000413186.2_Missense_Mutation_p.S140G|SYNE1_ENST00000448038.1_Missense_Mutation_p.S147G|SYNE1_ENST00000367248.3_Missense_Mutation_p.S147G|SYNE1_ENST00000423061.1_Missense_Mutation_p.S147G|SYNE1_ENST00000265368.4_Missense_Mutation_p.S140G|SYNE1_ENST00000341594.5_Missense_Mutation_p.S140G|SYNE1_ENST00000466159.2_Missense_Mutation_p.S140G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	140	Actin-binding.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGCAGGTTGCTGGTCAACTCT	0.448										HNSCC(10;0.0054)																																						0													81.0	71.0	75.0					6																	152831491		2203	4300	6503	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.418A>G	6.37:g.152831491T>C	ENSP00000356224:p.Ser140Gly		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	27.1	4.801117	0.90538	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	D;D;D;D;D;D;D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75	5.66	5.66	0.87406	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	D	0.95862	0.8653	L	0.45581	1.43	0.80722	D	1	D;D;D;D;D	0.76494	0.995;0.996;0.982;0.996;0.999	D;P;P;P;D	0.69142	0.962;0.87;0.816;0.87;0.958	D	0.96273	0.9200	10	0.54805	T	0.06	.	15.8952	0.79329	0.0:0.0:0.0:1.0	.	140;140;140;140;147	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	G	140;147;140;147;140;140;147;140;140;140	ENSP00000356224:S140G;ENSP00000396024:S147G;ENSP00000265368:S140G;ENSP00000390975:S147G;ENSP00000341887:S140G;ENSP00000356222:S140G;ENSP00000356217:S147G;ENSP00000414510:S140G;ENSP00000446021:S140G;ENSP00000441264:S140G	ENSP00000265368:S140G	S	-	1	0	SYNE1	152873184	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.166000	0.68216	0.519000	0.50382	AGC		0.448	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		35	45	35	45
CLN8	2055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	1728624	1728624	+	Missense_Mutation	SNP	A	A	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr8:1728624A>C	ENST00000331222.4	+	3	999	c.752A>C	c.(751-753)cAt>cCt	p.H251P	CLN8_ENST00000523237.1_3'UTR	NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	251	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				adult walking behavior (GO:0007628)|age-dependent response to oxidative stress (GO:0001306)|associative learning (GO:0008306)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|ceramide biosynthetic process (GO:0046513)|ceramide metabolic process (GO:0006672)|cholesterol metabolic process (GO:0008203)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|lipid biosynthetic process (GO:0008610)|lipid transport (GO:0006869)|lysosome organization (GO:0007040)|mitochondrial membrane organization (GO:0007006)|musculoskeletal movement (GO:0050881)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteolysis (GO:0045861)|negative regulation of transferase activity (GO:0051348)|nervous system development (GO:0007399)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|phospholipid metabolic process (GO:0006644)|photoreceptor cell maintenance (GO:0045494)|protein catabolic process (GO:0030163)|regulation of cell size (GO:0008361)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic motor neuron differentiation (GO:0021523)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		TATTGGACCCATAAGAAGACT	0.542																																					Pancreas(155;338 1942 6138 10888 50612)											0													158.0	141.0	147.0					8																	1728624		2203	4300	6503	SO:0001583	missense	2055			AF123761	CCDS5956.1	8p23.3	2014-09-17			ENSG00000182372	ENSG00000182372			2079	protein-coding gene	gene with protein product		607837	"""chromosome 8 open reading frame 61"""	EPMR, C8orf61		10508524	Standard	NM_018941		Approved	FLJ39417	uc003wpo.4	Q9UBY8	OTTHUMG00000090343	ENST00000331222.4:c.752A>C	8.37:g.1728624A>C	ENSP00000328182:p.His251Pro		Q86U71|Q96I95	Missense_Mutation	SNP	ENST00000331222.4	37	CCDS5956.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.532893	0.45073	.	.	ENSG00000182372	ENST00000331222	D	0.85088	-1.94	4.65	3.49	0.39957	TRAM/LAG1/CLN8 homology domain (3);	0.089964	0.43919	U	0.000502	D	0.88890	0.6560	M	0.65975	2.015	0.53688	D	0.999978	D	0.65815	0.995	D	0.63283	0.913	D	0.86849	0.2022	10	0.40728	T	0.16	-5.3596	10.0911	0.42447	0.9207:0.0:0.0793:0.0	.	251	Q9UBY8	CLN8_HUMAN	P	251	ENSP00000328182:H251P	ENSP00000328182:H251P	H	+	2	0	CLN8	1716031	1.000000	0.71417	0.894000	0.35097	0.097000	0.18754	6.633000	0.74286	0.813000	0.34350	0.528000	0.53228	CAT		0.542	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941		32	181	32	181
MLLT3	4300	hgsc.bcm.edu;ucsc.edu	37	9	20360828	20360828	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr9:20360828C>T	ENST00000380338.4	-	8	1629	c.1343G>A	c.(1342-1344)aGt>aAt	p.S448N	MLLT3_ENST00000475957.1_5'Flank|MLLT3_ENST00000429426.2_Missense_Mutation_p.S445N|MLLT3_ENST00000355930.6_Missense_Mutation_p.S42N|MLLT3_ENST00000380321.1_Missense_Mutation_p.S42N	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	448					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		GCTGCCATCACTTAAGCTAAC	0.418			T	MLL	ALL																																		Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	0													170.0	139.0	150.0					9																	20360828		2203	4300	6503	SO:0001583	missense	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.1343G>A	9.37:g.20360828C>T	ENSP00000369695:p.Ser448Asn		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Missense_Mutation	SNP	ENST00000380338.4	37	CCDS6494.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778414	0.90195	.	.	ENSG00000171843	ENST00000380338;ENST00000355930;ENST00000380323;ENST00000429426;ENST00000540751;ENST00000380321	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.82042	0.4951	M	0.72894	2.215	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.67900	0.954;0.954	T	0.81795	-0.0769	9	0.72032	D	0.01	-9.6659	20.6721	0.99693	0.0:1.0:0.0:0.0	.	445;448	B7Z755;P42568	.;AF9_HUMAN	N	448;42;42;445;487;42	.	ENSP00000348196:S42N	S	-	2	0	MLLT3	20350828	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.439000	0.73430	2.894000	0.99253	0.591000	0.81541	AGT		0.418	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		11	48	11	48
OR1L3	26735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	125437655	125437655	+	Missense_Mutation	SNP	G	G	A	rs142972365		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr9:125437655G>A	ENST00000304820.2	+	1	341	c.247G>A	c.(247-249)Gtg>Atg	p.V83M		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						AAAGATGCTCGTGAACTTCTT	0.398																																																0													163.0	160.0	161.0					9																	125437655		2203	4300	6503	SO:0001583	missense	26735				CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"""GPCR / Class A : Olfactory receptors"""	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.247G>A	9.37:g.125437655G>A	ENSP00000302863:p.Val83Met		B2RNF4|Q6IFN1	Missense_Mutation	SNP	ENST00000304820.2	37	CCDS35128.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.258311	0.23051	.	.	ENSG00000171481	ENST00000304820	T	0.01981	4.52	4.54	2.6	0.31112	GPCR, rhodopsin-like superfamily (1);	0.410486	0.17252	N	0.181120	T	0.02848	0.0085	L	0.60455	1.87	0.09310	N	1	B	0.19445	0.036	B	0.20384	0.029	T	0.39099	-0.9630	10	0.44086	T	0.13	-4.9212	4.6543	0.12610	0.2193:0.2958:0.4849:0.0	.	83	Q8NH93	OR1L3_HUMAN	M	83	ENSP00000302863:V83M	ENSP00000302863:V83M	V	+	1	0	OR1L3	124477476	0.000000	0.05858	0.887000	0.34795	0.935000	0.57460	-3.335000	0.00508	0.598000	0.29829	0.644000	0.83932	GTG		0.398	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1			61	163	61	163
MAGIX	79917	broad.mit.edu;ucsc.edu	37	X	49022446	49022446	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chrX:49022446G>A	ENST00000412696.2	+	6	713	c.713G>A	c.(712-714)gGa>gAa	p.G238E	MAGIX_ENST00000425661.2_Missense_Mutation_p.G162E|MAGIX_ENST00000376338.3_Missense_Mutation_p.G179E|MAGIX_ENST00000498742.1_3'UTR|MAGIX_ENST00000376339.1_Missense_Mutation_p.G174E	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	238																	CCAGATCCTGGAGGGCCGGAG	0.617																																																0													47.0	53.0	51.0					X																	49022446		2136	4221	6357	SO:0001583	missense	79917			AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.713G>A	X.37:g.49022446G>A	ENSP00000387928:p.Gly238Glu		A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	37	CCDS48106.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	16.04|16.04|16.04	3.010595|3.010595|3.010595	0.54361|0.54361|0.54361	.|.|.	.|.|.	ENSG00000017621|ENSG00000017621|ENSG00000017621	ENST00000415364|ENST00000376339;ENST00000425661;ENST00000412696;ENST00000376338;ENST00000425285;ENST00000454342|ENST00000458388	.|T;T;T;T;T;T|.	.|0.32515|.	.|1.97;2.25;1.89;1.79;1.66;1.45|.	3.86|3.86|3.86	2.98|2.98|2.98	0.34508|0.34508|0.34508	.|.|.	.|0.217441|.	.|0.23353|.	.|N|.	.|0.049104|.	T|T|.	0.25457|0.25457|.	0.0619|0.0619|.	L|L|L	0.27053|0.27053|0.27053	0.805|0.805|0.805	0.09310|0.09310|0.09310	N|N|N	0.999993|0.999993|0.999993	.|D;D;D;D;D|.	.|0.76494|.	.|0.999;0.997;0.999;0.999;0.999|.	.|D;P;D;D;D|.	.|0.69479|.	.|0.964;0.895;0.951;0.951;0.922|.	T|T|.	0.13442|0.13442|.	-1.0509|-1.0509|.	5|10|.	.|0.59425|.	.|D|.	.|0.04|.	-3.1638|-3.1638|-3.1638	5.572|5.572|5.572	0.17202|0.17202|0.17202	0.1525:0.0:0.8475:0.0|0.1525:0.0:0.8475:0.0|0.1525:0.0:0.8475:0.0	.|.|.	.|162;238;174;179;105|.	.|F8WCY7;Q9H6Y5;Q9H6Y5-3;Q9H6Y5-2;C9J123|.	.|.;MAGIX_HUMAN;.;.;.|.	K|E|X	202|174;162;238;179;179;105|162	.|ENSP00000365517:G174E;ENSP00000403515:G162E;ENSP00000387928:G238E;ENSP00000365516:G179E;ENSP00000411713:G179E;ENSP00000400147:G105E|.	.|ENSP00000365516:G179E|.	E|G|W	+|+|+	1|2|3	0|0|0	MAGIX|MAGIX|MAGIX	48909390|48909390|48909390	0.018000|0.018000|0.018000	0.18449|0.18449|0.18449	0.512000|0.512000|0.512000	0.27736|0.27736|0.27736	0.052000|0.052000|0.052000	0.14988|0.14988|0.14988	0.054000|0.054000|0.054000	0.14205|0.14205|0.14205	1.865000|1.865000|1.865000	0.54081|0.54081|0.54081	0.538000|0.538000|0.538000	0.68166|0.68166|0.68166	GAG|GGA|TGG		0.617	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859		31	78	31	78
COL4A5	1287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	107816843	107816843	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chrX:107816843C>T	ENST00000361603.2	+	9	749	c.505C>T	c.(505-507)Cca>Tca	p.P169S	COL4A5_ENST00000328300.6_Missense_Mutation_p.P169S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	169	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						ACTGCCAGGACCAAAGGGTAA	0.363									Alport syndrome with Diffuse Leiomyomatosis																																							0													132.0	124.0	127.0					X																	107816843		2203	4300	6503	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.505C>T	X.37:g.107816843C>T	ENSP00000354505:p.Pro169Ser		Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	C	0.738	-0.777479	0.02929	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.93189	-3.18;-3.18	5.25	4.37	0.52481	.	0.385415	0.27411	N	0.019500	D	0.90082	0.6902	L	0.52759	1.655	0.33149	D	0.545478	B;B	0.27882	0.192;0.192	B;B	0.25614	0.062;0.062	D	0.88586	0.3140	10	0.21540	T	0.41	.	14.6349	0.68682	0.1468:0.8532:0.0:0.0	.	169;169	E7EVY4;P29400	.;CO4A5_HUMAN	S	169	ENSP00000331902:P169S;ENSP00000354505:P169S	ENSP00000331902:P169S	P	+	1	0	COL4A5	107703499	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	4.001000	0.57046	1.090000	0.41315	-0.330000	0.08379	CCA		0.363	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			54	157	54	157
HSP90AB2P	391634	broad.mit.edu;ucsc.edu	37	4	13339453	13339453	+	RNA	SNP	G	G	A	rs16898654	byFrequency	TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr4:13339453G>A	ENST00000602906.1	+	0	862							Q58FF8	H90B2_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 2, pseudogene						protein folding (GO:0006457)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			kidney(3)|lung(1)	4						GATGCCACCCGTCTGAGCTGC	0.428													A|||	386	0.0770767	0.2534	0.0317	5008	,	,		21633	0.0		0.0189	False		,,,				2504	0.0102															0																																												391634			AY956763		4p15.33	2012-04-18	2011-04-15		ENSG00000205940	ENSG00000205940			32537	pseudogene	pseudogene			"""heat shock protein 90kDa alpha (cytosolic), class B member 2 (pseudogene)"""			16269234	Standard	NG_032979		Approved	HSP90BB		Q58FF8			4.37:g.13339453G>A				RNA	SNP	ENST00000602906.1	37																																																																																					0.428	HSP90AB2P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000359156.2			9	15	9	15
SLC22A8	9376	broad.mit.edu;ucsc.edu	37	11	62763251	62763251	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr11:62763251T>C	ENST00000336232.2	-	7	1061	c.926A>G	c.(925-927)aAg>aGg	p.K309R	SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000311438.8_Missense_Mutation_p.K309R|SLC22A8_ENST00000545207.1_Missense_Mutation_p.K218R|SLC22A8_ENST00000430500.2_Missense_Mutation_p.K309R|SLC22A8_ENST00000535878.1_Missense_Mutation_p.K186R	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	309					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GTACTTGGCCTTGGCCAAGGA	0.597																																																0													164.0	151.0	155.0					11																	62763251		2201	4298	6499	SO:0001583	missense	9376			AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"""Solute carriers"""	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.926A>G	11.37:g.62763251T>C	ENSP00000337335:p.Lys309Arg		B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	37	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.038211	0.54896	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	5.07	5.07	0.68467	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.858758	0.09946	N	0.735274	T	0.60573	0.2279	M	0.62723	1.935	0.35580	D	0.806195	P;P	0.36171	0.485;0.541	B;B	0.42214	0.261;0.38	T	0.60214	-0.7307	10	0.26408	T	0.33	.	11.2452	0.48993	0.0:0.0:0.0:1.0	.	309;309	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	R	309;295;218;186;309;309	ENSP00000337335:K309R;ENSP00000441658:K218R;ENSP00000443368:K186R;ENSP00000311463:K309R;ENSP00000398548:K309R	ENSP00000311463:K309R	K	-	2	0	SLC22A8	62519827	0.998000	0.40836	1.000000	0.80357	0.839000	0.47603	3.141000	0.50593	1.898000	0.54952	0.374000	0.22700	AAG		0.597	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		80	169	80	169
SI	6476	broad.mit.edu;ucsc.edu	37	3	164767582	164767582	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr3:164767582G>A	ENST00000264382.3	-	14	1656	c.1594C>T	c.(1594-1596)Cct>Tct	p.P532S		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	532	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	ATTTTACCAGGAGTAAACGGT	0.264										HNSCC(35;0.089)																																						0													82.0	91.0	88.0					3																	164767582		2203	4287	6490	SO:0001583	missense	6476			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1594C>T	3.37:g.164767582G>A	ENSP00000264382:p.Pro532Ser		A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880810	0.72294	.	.	ENSG00000090402	ENST00000264382	D	0.90504	-2.68	5.58	5.58	0.84498	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96836	0.8967	H	0.95043	3.615	0.58432	D	0.999996	D	0.76494	0.999	D	0.69479	0.964	D	0.97766	1.0223	10	0.87932	D	0	.	18.5615	0.91101	0.0:0.0:1.0:0.0	.	532	P14410	SUIS_HUMAN	S	532	ENSP00000264382:P532S	ENSP00000264382:P532S	P	-	1	0	SI	166250276	1.000000	0.71417	0.994000	0.49952	0.458000	0.32498	9.114000	0.94329	2.622000	0.88805	0.585000	0.79938	CCT		0.264	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		17	58	17	58
SYNJ2	8871	broad.mit.edu;hgsc.bcm.edu	37	6	158504625	158504627	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr6:158504625_158504627delAGA	ENST00000355585.4	+	21	3105_3107	c.3030_3032delAGA	c.(3028-3033)tcagaa>tca	p.E1011del	SYNJ2_ENST00000367112.1_In_Frame_Del_p.E96del|SYNJ2_ENST00000367122.2_In_Frame_Del_p.E1011del|SYNJ2_ENST00000367121.3_In_Frame_Del_p.E1011del	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1011					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		ACTATGAGTCAGAAGGTTAGTGA	0.517																																																0																																										SO:0001651	inframe_deletion	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.3030_3032delAGA	6.37:g.158504625_158504627delAGA	ENSP00000347792:p.Glu1011del		Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	In_Frame_Del	DEL	ENST00000355585.4	37	CCDS5254.1																																																																																				0.517	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			33	142	33	142
KMT2C	58508	broad.mit.edu;hgsc.bcm.edu	37	7	151845685	151845686	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr7:151845685_151845686delGA	ENST00000262189.6	-	52	13544_13545	c.13326_13327delTC	c.(13324-13329)actcagfs	p.Q4443fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.Q4500fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4443					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GCACCAGCCTGAGTCTCATAGA	0.515																																																0																																										SO:0001589	frameshift_variant	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13326_13327delTC	7.37:g.151845685_151845686delGA	ENSP00000262189:p.Gln4443fs		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																				0.515	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			37	177	37	177
UCK1	83549	broad.mit.edu;hgsc.bcm.edu	37	9	134404915	134404915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr9:134404915delT	ENST00000372215.4	-	3	418	c.325delA	c.(325-327)acgfs	p.T109fs	UCK1_ENST00000372210.3_Frame_Shift_Del_p.T100fs|UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372208.3_Frame_Shift_Del_p.T109fs|UCK1_ENST00000372211.3_Frame_Shift_Del_p.T114fs	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	109					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		ACCTCCACCGTTTTGCCCTCC	0.557																																					Melanoma(42;523 1129 28385 43975 48113)											0													303.0	252.0	269.0					9																	134404915		2203	4300	6503	SO:0001589	frameshift_variant	83549			AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.325delA	9.37:g.134404915delT	ENSP00000361289:p.Thr109fs		Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Frame_Shift_Del	DEL	ENST00000372215.4	37	CCDS6944.1																																																																																				0.557	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432		47	115	47	115
LRRC43	254050	broad.mit.edu;hgsc.bcm.edu	37	12	122677545	122677545	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr12:122677545delC	ENST00000339777.4	+	7	1371	c.1343delC	c.(1342-1344)tccfs	p.S448fs	LRRC43_ENST00000425921.1_Frame_Shift_Del_p.S263fs	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	448										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CTCTGCCCGTCCCCAGGGTAA	0.577																																																0													29.0	31.0	30.0					12																	122677545		1951	4140	6091	SO:0001589	frameshift_variant	254050			AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.1343delC	12.37:g.122677545delC	ENSP00000344233:p.Ser448fs		Q6ZVT9	Frame_Shift_Del	DEL	ENST00000339777.4	37	CCDS45001.1																																																																																				0.577	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		10	35	10	35
HTR2A	3356	broad.mit.edu;hgsc.bcm.edu	37	13	47409749	47409750	+	Frame_Shift_Del	DEL	AA	AA	-	rs143289722		TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr13:47409749_47409750delAA	ENST00000378688.4	-	3	769_770	c.638_639delTT	c.(637-639)tttfs	p.F213fs	HTR2A_ENST00000543956.1_Frame_Shift_Del_p.F129fs|HTR2A_ENST00000542664.1_Frame_Shift_Del_p.F213fs			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	213					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CCTGTAGCCCAAAGACTGGTAT	0.396																																																0																																										SO:0001589	frameshift_variant	3356			X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5293	protein-coding gene	gene with protein product		182135	"""5-hydroxytryptamine (serotonin) receptor 2A"""	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.638_639delTT	13.37:g.47409749_47409750delAA	ENSP00000367959:p.Phe213fs		B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Frame_Shift_Del	DEL	ENST00000378688.4	37	CCDS9405.1																																																																																				0.396	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		22	86	22	86
TYK2	7297	broad.mit.edu;hgsc.bcm.edu	37	19	10479066	10479067	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr19:10479066_10479067delAA	ENST00000525621.1	-	4	702_703	c.221_222delTT	c.(220-222)tttfs	p.F74fs	TYK2_ENST00000529370.1_Frame_Shift_Del_p.F74fs|TYK2_ENST00000264818.6_Frame_Shift_Del_p.F74fs|TYK2_ENST00000524462.1_Intron	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	74	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			CGAAGAGGGCAAAGAGATTGAA	0.54																																																0																																										SO:0001589	frameshift_variant	7297				CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.221_222delTT	19.37:g.10479066_10479067delAA	ENSP00000431885:p.Phe74fs		Q6QB10|Q96CH0	Frame_Shift_Del	DEL	ENST00000525621.1	37	CCDS12236.1																																																																																				0.540	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1			48	110	48	110
LGALS13	29124	broad.mit.edu;hgsc.bcm.edu	37	19	40097866	40097868	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr19:40097866_40097868delAAG	ENST00000221797.4	+	4	352_354	c.307_309delAAG	c.(307-309)aagdel	p.K103del		NM_013268.2	NP_037400.1	Q9UHV8	PP13_HUMAN	lectin, galactoside-binding, soluble, 13	103	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CTTGTAGATAAAGGTCAATGGCA	0.458																																																0																																										SO:0001651	inframe_deletion	29124			AF117383	CCDS33024.1	19q13.2	2014-03-19	2008-07-25		ENSG00000105198	ENSG00000105198		"""Lectins, galactoside-binding"""	15449	protein-coding gene	gene with protein product	"""galectin 13"""	608717				6856484, 10527825	Standard	NM_013268		Approved	PP13, PLAC8	uc002omb.3	Q9UHV8	OTTHUMG00000183073	ENST00000221797.4:c.307_309delAAG	19.37:g.40097866_40097868delAAG	ENSP00000221797:p.Lys103del		C5HZ15	In_Frame_Del	DEL	ENST00000221797.4	37	CCDS33024.1																																																																																				0.458	LGALS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464968.1	NM_013268		31	40	31	40
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42796905	42796906	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-E1-5319-01A-01D-1893-08	TCGA-E1-5319-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d252a54e-0377-4b3e-8228-26108ea704fa	1121c5c3-e239-4edf-aa09-af5dbfabaaea	g.chr19:42796905_42796906delTG	ENST00000575354.2	+	14	3403_3404	c.3363_3364delTG	c.(3361-3366)actgtgfs	p.V1122fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.V1121fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.V2030fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1122	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)				TGGTCTACACTGTGGCCACCAG	0.668			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										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.3363_3364delTG	19.37:g.42796907_42796908delTG	ENSP00000458663:p.Val1122fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.668	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			26	73	26	73
