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	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
SSH1	54434	broad.mit.edu	hg19	12	109182113	109182113	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr12:109182113C>T	ENST00000326495.5	-	15	2894	c.2801G>A	c.(2800-2802)cGg>cAg	p.R934Q	SSH1_ENST00000360239.3_Missense_Mutation_p.R622Q	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	934	Interaction with YWHAG.	actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					GCTGGAGCTCCGGGTCAGGTT	0.597	0	57.0	61.0	60.0	12	109182113	2197	4295	6492	SO:0001583	missense	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""		10718198, 11832213	Standard	NM_018984	Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.2801G>A	12.37:g.109182113C>T	ENSP00000315713:p.Arg934Gln	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	31	5.065292	0.93898	.	.	ENSG00000084112	ENST00000360239;ENST00000326495	T;T	0.16897	2.41;2.31	5.44	4.55	0.56014	.	0.152283	0.64402	D	0.000011	T	0.40694	0.1127	M	0.70275	2.135	0.41014	D	0.98502	D;D	0.89917	0.999;1.0	P;D	0.83275	0.715;0.996	T	0.27739	-1.0065	10	0.45353	T	0.12	-29.3895	14.4201	0.67177	0.0:0.9284:0.0:0.0716	.	934;622	Q8WYL5;Q8WYL5-4	SSH1_HUMAN;.	Q	622;934	ENSP00000353374:R622Q;ENSP00000315713:R934Q	ENSP00000315713:R934Q	R	-	2	0	SSH1	107706242	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	7.452000	0.80683	1.307000	0.44944	0.650000	0.86243	CGG	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1		101.826087	0	-9	81	0	0	1	0	NM_018984	31	101.826087	31	0.500000
LUZP1	7798	broad.mit.edu	hg19	1	23418504	23418504	+	Missense_Mutation	SNP	G	G	A	rs146031719	byFrequency	TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr1:23418504G>A	ENST00000302291.4	-	4	3052	c.2251C>T	c.(2251-2253)Cgg>Tgg	p.R751W	LUZP1_ENST00000418342.1_Missense_Mutation_p.R751W|LUZP1_ENST00000374623.3_Missense_Mutation_p.R751W|LUZP1_ENST00000314174.5_Missense_Mutation_p.R751W			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	751			nucleus		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)	GCTCTAGACCGCAACGCCTCT	0.478	0	135.0	143.0	140.0	1	23418504	2203	4300	6503	SO:0001583	missense	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641		14985	protein-coding gene	gene with protein product		601422			8812416	Standard	NM_033631	Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.2251C>T	1.37:g.23418504G>A	ENSP00000303758:p.Arg751Trp	Q5TH93|Q8N4X3|Q8TEH1	ENST00000302291.4	37	CCDS30628.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461067	0.63513	2.27E-4	1.16E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.19105	2.37;2.37;2.37;2.17	5.27	3.37	0.38596	.	0.158849	0.29707	N	0.011415	T	0.19287	0.0463	L	0.57536	1.79	0.28033	N	0.93406	B;B	0.26876	0.083;0.162	B;B	0.21917	0.027;0.037	T	0.12604	-1.0541	10	0.51188	T	0.08	.	7.6254	0.28210	0.0802:0.0:0.6097:0.31	.	751;751	Q86V48-2;Q86V48	.;LUZP1_HUMAN	W	751	ENSP00000393460:R751W;ENSP00000363752:R751W;ENSP00000303758:R751W;ENSP00000313705:R751W	ENSP00000303758:R751W	R	-	1	2	LUZP1	23291091	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	2.382000	0.44345	1.211000	0.43351	0.485000	0.47835	CGG	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3		-32.337774	0	3	189	0	0	1	0	NM_033631	4	7.117834	154	0.025316
WDR66	144406	broad.mit.edu	hg19	12	122392079	122392079	+	Silent	SNP	A	A	G			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr12:122392079A>G	ENST00000288912.4	+	10	2228	c.1374A>G	c.(1372-1374)ttA>ttG	p.L458L	WDR66_ENST00000397454.2_Silent_p.L458L	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	458				calcium ion binding	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)	ACTTGAATTTAACACAAATAC	0.413	0	98.0	94.0	95.0	12	122392079	1897	4120	6017	SO:0001819	synonymous_variant	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023	"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product					17967944	Standard	NM_001178003	Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000397454.2:c.1374A>G	12.37:g.122392079A>G		C9J1W2|Q8IYA3|Q8N898|Q8NDE7	ENST00000397454.2	37	CCDS53840.1																																																																																			WDR66-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401701.1		176.800787	0	6	126	0	0	1	0	NM_144668	52	177.204359	39	0.571429
COL18A1	80781	broad.mit.edu	hg19	21	46930115	46930115	+	Silent	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr21:46930115G>A	ENST00000359759.4	+	39	4899	c.4878G>A	c.(4876-4878)caG>caA	p.Q1626Q	COL18A1_ENST00000400337.2_Silent_p.Q1211Q|COL18A1_ENST00000355480.5_Silent_p.Q1391Q|SLC19A1_ENST00000567670.1_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1626	Nonhelical region 11 (NC11).	cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding	breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)	CGCGCCTGCAGGACCTGTACA	0.726	0	8.0	11.0	10.0	21	46930115	2006	4132	6138	SO:0001819	synonymous_variant		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871	"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO	8188291, 8776601, 10942434, 17546652	Standard	NM_130445	Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4878G>A	21.37:g.46930115G>A		A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	G	9.305	1.053998	0.19907	.	.	ENSG00000182871	ENST00000423214	.	.	.	4.46	1.57	0.23409	.	.	.	.	.	T	0.55721	0.1938	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48222	-0.9054	4	.	.	.	.	8.1174	0.30950	0.3609:0.0:0.6391:0.0	.	.	.	.	K	196	.	.	R	+	2	0	COL18A1	45754543	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	0.958000	0.29227	0.444000	0.26612	-0.137000	0.14449	AGG	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		12.701495	0	3	14	0	0	1	0		4	12.848921	2	0.666667
MRPL4	51073	broad.mit.edu	hg19	19	10365278	10365278	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr19:10365278C>T	ENST00000393733.2	+	4	316	c.289C>T	c.(289-291)Cac>Tac	p.H97Y	MRPL4_ENST00000588502.1_Missense_Mutation_p.H96Y|MRPL4_ENST00000253099.6_Missense_Mutation_p.H97Y|CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000590669.1_Missense_Mutation_p.H97Y|MRPL4_ENST00000307422.5_Missense_Mutation_p.H97Y			Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	97		translation	mitochondrion|ribosome	structural constituent of ribosome	breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)	GGACATACTGCACCAGGTTGC	0.537	0	225.0	208.0	214.0	19	10365278	2203	4300	6503	SO:0001583	missense	AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364	"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823				Standard	NM_015956	Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.289C>T	19.37:g.10365278C>T	ENSP00000253099:p.His97Tyr	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	ENST00000253099.6	37	CCDS12230.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205545	0.58234	.	.	ENSG00000105364	ENST00000253099;ENST00000307422;ENST00000393733	.	.	.	4.78	2.65	0.31530	Ribosomal protein L4 domain (1);	0.053696	0.64402	D	0.000001	T	0.67998	0.2953	M	0.70275	2.135	0.51012	D	0.999909	D;D	0.62365	0.972;0.991	P;P	0.61722	0.828;0.893	T	0.66956	-0.5792	9	0.52906	T	0.07	-27.9053	9.1055	0.36696	0.0:0.8186:0.0:0.1814	.	97;97	Q9BYD3-2;Q9BYD3	.;RM04_HUMAN	Y	97	.	ENSP00000253099:H97Y	H	+	1	0	MRPL4	10226278	1.000000	0.71417	0.959000	0.39883	0.352000	0.29268	4.944000	0.63561	0.545000	0.28902	0.555000	0.69702	CAC	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1		182.447738	0	29	247	0	0	1	0		61	183.062543	81	0.429577
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		106.393341	0	2	114	0	0	1	0	NM_002072	32	106.586611	40	0.444444
FGFR2	2263	broad.mit.edu	hg19	10	123298226	123298226	+	Nonsense_Mutation	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr10:123298226G>A	ENST00000358487.5	-	6	900	c.628C>T	c.(628-630)Cga>Tga	p.R210*	FGFR2_ENST00000369060.4_Nonsense_Mutation_p.R210*|FGFR2_ENST00000356226.4_Nonsense_Mutation_p.R95*|FGFR2_ENST00000351936.6_Nonsense_Mutation_p.R210*|FGFR2_ENST00000369056.1_Nonsense_Mutation_p.R210*|FGFR2_ENST00000346997.2_Nonsense_Mutation_p.R210*|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369061.4_Nonsense_Mutation_p.R210*|FGFR2_ENST00000359354.2_Nonsense_Mutation_p.R210*|FGFR2_ENST00000369059.1_Nonsense_Mutation_p.R95*|FGFR2_ENST00000357555.5_Nonsense_Mutation_p.R121*|FGFR2_ENST00000457416.2_Nonsense_Mutation_p.R210*|FGFR2_ENST00000360144.3_Nonsense_Mutation_p.R121*	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	210	Ig-like C2-type 2.	angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding	breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	TGCTGGTTTCGTACCTGAAAA	0.423	0	136.0	119.0	124.0	10	123298226	2203	4300	6503	SO:0001587	stop_gained	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS		Standard	NM_022970	Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000457416.2:c.628C>T	10.37:g.123298226G>A	ENSP00000410294:p.Arg210*	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	ENST00000457416.2	37	CCDS7620.2	.	.	.	.	.	.	.	.	.	.	G	42	9.173824	0.99089	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	X	121;210;210;210;95;210;95;210;210;210;121;210;210;121;210	.	ENSP00000337665:R121X	R	-	1	2	FGFR2	123288216	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	7.751000	0.85126	2.941000	0.99782	0.655000	0.94253	CGA	FGFR2-010	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050724.1		96.550267	0	-7	85	0	0	1	0	NM_022976, NM_000141	30	96.553776	31	0.491803
TRERF1	55809	broad.mit.edu	hg19	6	42196196	42196196	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr6:42196196C>T	ENST00000541110.1	-	18	4118	c.3550G>A	c.(3550-3552)Gac>Aac	p.D1184N	TRERF1_ENST00000372922.4_Missense_Mutation_p.D1164N|TRERF1_ENST00000340840.2_Missense_Mutation_p.D1093N|TRERF1_ENST00000354325.2_Missense_Mutation_p.D1081N|TRERF1_ENST00000372917.4_Missense_Mutation_p.D1093N			Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1164	Interacts with CREBBP.	cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding	breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		ACGACGTCGTCGTCGAGGATG	0.577	1	150.0	143.0	145.0	6	42196196	2203	4300	6503	SO:0001583	missense	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496		18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2	11349124	Standard	XM_005249223	Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3490G>A	6.37:g.42196196C>T	ENSP00000362013:p.Asp1164Asn	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803405	0.50315	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12879	2.82;2.64;2.84;2.64;2.64	5.78	4.89	0.63831	.	0.529823	0.18083	N	0.152222	T	0.03011	0.0089	N	0.14661	0.345	0.09310	N	1	B;B;B;B;P	0.51791	0.013;0.007;0.007;0.013;0.948	B;B;B;B;B	0.42771	0.003;0.001;0.001;0.003;0.397	T	0.28138	-1.0053	10	0.37606	T	0.19	-4.353	7.4591	0.27285	0.0:0.7183:0.1413:0.1405	.	1081;1184;1164;920;932	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	N	1184;1093;1164;1093;1081	ENSP00000439689:D1184N;ENSP00000362008:D1093N;ENSP00000362013:D1164N;ENSP00000339438:D1093N;ENSP00000346285:D1081N	ENSP00000339438:D1093N	D	-	1	0	TRERF1	42304174	0.038000	0.19896	0.003000	0.11579	0.602000	0.36980	2.109000	0.41863	1.411000	0.46957	0.563000	0.77884	GAC	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2		136.137258	0	-5	157	0	0	1	0	NM_033502	54	148.769953	164	0.247706
FASTKD3	79072	broad.mit.edu	hg19	5	7859575	7859575	+	Silent	SNP	T	T	C			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr5:7859575T>C	ENST00000264669.5	-	7	2098	c.1962A>G	c.(1960-1962)caA>caG	p.Q654Q	FASTKD3_ENST00000513658.1_5'UTR|MTRR_ENST00000502509.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	654		apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity	breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					GAACAGTGTTTTGAGAAAACA	0.318	0	86.0	86.0	86.0	5	7859575	2202	4298	6500	SO:0001819	synonymous_variant	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279		28758	protein-coding gene	gene with protein product					12477932	Standard	NM_024091	Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1962A>G	5.37:g.7859575T>C		Q9BVD3	ENST00000264669.5	37	CCDS3873.1																																																																																			FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1		50.491754	0	11	86	0	0	1	0	NM_024091	16	50.841651	24	0.400000
SLC6A13	6540	broad.mit.edu	hg19	12	333591	333591	+	Silent	SNP	G	G	A	rs145951312		TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr12:333591G>A	ENST00000343164.4	-	10	1201	c.1149C>T	c.(1147-1149)gtC>gtT	p.V383V	SLC6A13_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Silent_p.V291V	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	383		neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity	NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)		CCAGGAGAACGACCATGAAGA	0.597	0	124.0	111.0	115.0	12	333591	2203	4300	6503	SO:0001819	synonymous_variant	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379	"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""			Standard	NM_001243392	Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1149C>T	12.37:g.333591G>A		B4DJL1|Q8TCC2|Q8WW56	ENST00000343164.4	37	CCDS8502.1																																																																																			SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1		62.596552	0	5	78	0	0	1	0	NM_016615	20	62.642051	23	0.465116
ALG9	79796	broad.mit.edu	hg19	11	111715342	111715342	+	Silent	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr11:111715342G>A	ENST00000398006.2	-	9	1395	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000531154.1_Silent_p.L163L|ALG9_ENST00000527228.1_5'UTR	NM_001077690.1|NM_001077691.1|NM_001077692.1	NP_001071158.1|NP_001071159.1|NP_001071160.1	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	334		dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity	endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)	CTCTGCAGCAGGTATTCCATA	0.403	0	118.0	108.0	111.0	11	111715342	1877	4116	5993	SO:0001819	synonymous_variant		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	15672	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dol-P-Man dependent alpha-1,2-mannosyltransferase"""	606941	"""disrupted in bipolar affective disorder 1"", ""asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"""	DIBD1	12030331, 15148656	Standard	NM_024740	Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.487C>T	11.37:g.111715342G>A		Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	ENST00000531154.1	37	CCDS41714.1																																																																																			ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1		257.574635	0	24	222	0	0	1	0	NM_024740	80	257.703494	90	0.470588
AMZ1	155185	broad.mit.edu	hg19	7	2740257	2740257	+	Missense_Mutation	SNP	C	C	G			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr7:2740257C>G	ENST00000312371.4	+	2	540	c.172C>G	c.(172-174)Ctg>Gtg	p.L58V	AMZ1_ENST00000407112.1_Missense_Mutation_p.L58V	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	58				metallopeptidase activity|zinc ion binding	breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)	CTTCTGCACCCTGCTCATCCG	0.677	0	95.0	102.0	100.0	7	2740257	2203	4300	6503	SO:0001583	missense	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945		22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168			15972818	Standard	NM_133463	Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.172C>G	7.37:g.2740257C>G	ENSP00000308149:p.Leu58Val	B3KRS0|Q8TF51	ENST00000312371.4	37	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464523	0.63513	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.16597	2.33;2.33	4.34	3.21	0.36854	.	0.286891	0.24368	N	0.039133	T	0.27765	0.0683	M	0.65975	2.015	0.29654	N	0.843744	D;P	0.58268	0.982;0.939	P;B	0.54889	0.763;0.433	T	0.04767	-1.0928	10	0.34782	T	0.22	-16.3083	9.3477	0.38118	0.0:0.8156:0.0:0.1844	.	58;58	B3KRS0;Q400G9	.;AMZ1_HUMAN	V	58	ENSP00000308149:L58V;ENSP00000386020:L58V	ENSP00000308149:L58V	L	+	1	2	AMZ1	2706783	0.485000	0.25972	0.811000	0.32455	0.926000	0.56050	0.836000	0.27545	1.969000	0.57287	0.561000	0.74099	CTG	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1		159.147655	0	32	177	0	0	1	0	NM_133463	50	159.149811	49	0.505051
BAZ2A	11176	broad.mit.edu	hg19	12	57003582	57003582	+	Missense_Mutation	SNP	A	A	C			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr12:57003582A>C	ENST00000179765.5	-	11	2139	c.1940T>G	c.(1939-1941)gTc>gGc	p.V647G	BAZ2A_ENST00000549884.1_Missense_Mutation_p.V677G|BAZ2A_ENST00000379441.3_Missense_Mutation_p.V649G|BAZ2A_ENST00000551812.1_Missense_Mutation_p.V679G			Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	679		chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding	breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31					AGTGATTTTGACCTTAGGTGG	0.512	0	79.0	75.0	76.0	12	57003582	1903	4120	6023	SO:0001583	missense	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108	"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682			10662543, 11532953	Standard	XM_005268596	Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000549884.1:c.2030T>G	12.37:g.57003582A>C	ENSP00000447941:p.Val677Gly	B3KN66|O00536|O15030|Q68DI8|Q96H26	ENST00000549884.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.97|14.97	2.694188|2.694188	0.48202|0.48202	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000547650|ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	.|T;T;T;T	.|0.30981	.|2.3;2.3;1.51;2.3	5.02|5.02	5.02|5.02	0.67125|0.67125	.|AT hook, DNA-binding motif (1);	.|0.520684	.|0.20307	.|N	.|0.094906	T|T	0.36303|0.36303	0.0962|0.0962	L|L	0.43923|0.43923	1.385|1.385	0.58432|0.58432	D|D	0.999996|0.999996	.|P;P	.|0.46220	.|0.874;0.8	.|P;B	.|0.48227	.|0.571;0.368	T|T	0.17961|0.17961	-1.0352|-1.0352	5|10	.|0.87932	.|D	.|0	.|.	14.1547|14.1547	0.65410|0.65410	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|677;679	.|F8VU39;Q9UIF9	.|.;BAZ2A_HUMAN	A|G	105|649;647;679;677	.|ENSP00000368754:V649G;ENSP00000179765:V647G;ENSP00000446880:V679G;ENSP00000447941:V677G	.|ENSP00000179765:V647G	S|V	-|-	1|2	0|0	BAZ2A|BAZ2A	55289849|55289849	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.868000|0.868000	0.49771|0.49771	3.441000|3.441000	0.52893|0.52893	2.243000|2.243000	0.73865|0.73865	0.533000|0.533000	0.62120|0.62120	TCA|GTC	BAZ2A-003	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000408563.1		19.817705	0	16	46	0	0	1	0	NM_013449	7	20.334466	14	0.333333
ESRRG	2104	broad.mit.edu	hg19	1	216692613	216692613	+	Missense_Mutation	SNP	T	T	C			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr1:216692613T>C	ENST00000391890.3	-	8	1482	c.965A>G	c.(964-966)aAa>aGa	p.K322R	ESRRG_ENST00000360012.3_Missense_Mutation_p.K315R|ESRRG_ENST00000493603.1_Missense_Mutation_p.K315R|ESRRG_ENST00000366937.1_Missense_Mutation_p.K350R|ESRRG_ENST00000359162.2_Missense_Mutation_p.K315R|ESRRG_ENST00000361525.3_Missense_Mutation_p.K315R|ESRRG_ENST00000366940.2_Missense_Mutation_p.K315R|ESRRG_ENST00000487276.1_Missense_Mutation_p.K315R|ESRRG_ENST00000408911.3_Missense_Mutation_p.K338R|ESRRG_ENST00000463665.1_Missense_Mutation_p.K276R|ESRRG_ENST00000493748.1_Missense_Mutation_p.K315R|ESRRG_ENST00000366938.2_Missense_Mutation_p.K315R|ESRRG_ENST00000361395.2_Missense_Mutation_p.K315R	NM_001243515.1|NM_001243519.1	NP_001230444.1|NP_001230448.1	P62508	ERR3_HUMAN	estrogen-related receptor gamma	338		positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	GCCTGCTAATTTGGACTGGTC	0.403	0	102.0	97.0	99.0	1	216692613	2203	4300	6503	SO:0001583	missense	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482	"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969			9676434, 10072763	Standard	NM_001243505	Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000366937.1:c.1049A>G	1.37:g.216692613T>C	ENSP00000355904:p.Lys350Arg	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	ENST00000366937.1	37	CCDS58061.1	.	.	.	.	.	.	.	.	.	.	T	6.099	0.386571	0.11524	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17	5.82	5.82	0.92795	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.87609	0.6220	N	0.01640	-0.785	0.80722	D	1	B;B;B	0.11235	0.0;0.004;0.002	B;B;B	0.09377	0.002;0.004;0.004	D	0.84625	0.0686	10	0.10902	T	0.67	.	16.1814	0.81903	0.0:0.0:0.0:1.0	.	276;350;338	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	R	315;315;350;338;315;315;315;315;315;322;276;315;315;315;315	ENSP00000355225:K315R;ENSP00000355907:K315R;ENSP00000355904:K350R;ENSP00000386171:K338R;ENSP00000352077:K315R;ENSP00000354584:K315R;ENSP00000355905:K315R;ENSP00000353108:K315R;ENSP00000419594:K315R;ENSP00000375761:K322R;ENSP00000418629:K276R;ENSP00000419155:K315R;ENSP00000417374:K315R;ENSP00000419514:K315R	ENSP00000346386:K315R	K	-	2	0	ESRRG	214759236	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.013000	0.88655	2.234000	0.73211	0.533000	0.62120	AAA	ESRRG-006	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000089881.4		122.335638	0	20	72	0	0	1	0	NM_206595	37	122.339072	38	0.493333
WDHD1	11169	broad.mit.edu	hg19	14	55424348	55424348	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr14:55424348C>T	ENST00000360586.3	-	22	2772	c.2707G>A	c.(2707-2709)Gtt>Att	p.V903I	WDHD1_ENST00000420358.2_Missense_Mutation_p.V780I|WDHD1_ENST00000421192.1_Missense_Mutation_p.V780I|WDHD1_ENST00000359167.4_Missense_Mutation_p.V421I	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	903			cytoplasm|nucleoplasm	DNA binding	breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42					CTAAAGGTAACTGCACCTTTC	0.303	0	58.0	56.0	56.0	14	55424348	2203	4300	6503	SO:0001583	missense	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554	"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126			9175701, 20028748	Standard	NM_007086	Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.2707G>A	14.37:g.55424348C>T	ENSP00000353793:p.Val903Ile	C9JW18|F6W0U7	ENST00000360586.3	37	CCDS9721.1	.	.	.	.	.	.	.	.	.	.	C	6.382	0.438550	0.12104	.	.	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.62232	0.39;0.91;0.04	4.84	3.01	0.34805	.	0.400816	0.24236	N	0.040319	T	0.43366	0.1244	L	0.28115	0.83	0.26354	N	0.977152	B;B	0.17667	0.023;0.007	B;B	0.16289	0.015;0.007	T	0.20571	-1.0271	10	0.25106	T	0.35	.	7.3723	0.26808	0.0:0.6629:0.0:0.3371	.	421;903	F8W7P7;O75717	.;WDHD1_HUMAN	I	903;421;780	ENSP00000353793:V903I;ENSP00000352085:V421I;ENSP00000391049:V780I	ENSP00000352085:V421I	V	-	1	0	WDHD1	54494098	1.000000	0.71417	0.998000	0.56505	0.882000	0.50991	2.000000	0.40816	1.048000	0.40298	-0.379000	0.06801	GTT	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2		49.555636	0	30	94	0	0	1	0	NM_007086	17	49.819076	24	0.414634
SEMA6D	80031	broad.mit.edu	hg19	15	48058164	48058164	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr15:48058164G>A	ENST00000316364.5	+	14	1965	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H	SEMA6D_ENST00000354744.4_Missense_Mutation_p.R509H|SEMA6D_ENST00000558816.1_Missense_Mutation_p.R509H|SEMA6D_ENST00000537942.1_Missense_Mutation_p.R509H|SEMA6D_ENST00000536845.2_Missense_Mutation_p.R509H|SEMA6D_ENST00000355997.3_Missense_Mutation_p.R509H|SEMA6D_ENST00000358066.4_Missense_Mutation_p.R509H|SEMA6D_ENST00000558014.1_Missense_Mutation_p.R509H|SEMA6D_ENST00000389428.3_Missense_Mutation_p.R509H|SEMA6D_ENST00000389432.2_Missense_Mutation_p.R509H|SEMA6D_ENST00000389433.2_Missense_Mutation_p.R509H	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	509	Sema.	axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity	biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)	TGCATTATCCGCATCCCCCTC	0.443	0	228.0	206.0	213.0	15	48058164	2198	4297	6495	SO:0001583	missense	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872	"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295			12110693, 14977921	Standard	NM_020858	Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1526G>A	15.37:g.48058164G>A	ENSP00000324857:p.Arg509His	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	ENST00000316364.5	37	CCDS32225.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.14	3.312884	0.60414	2.27E-4	0.0	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997	T;T;T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83	5.88	5.88	0.94601	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	L	0.53671	1.685	0.80722	D	1	P;B;P;B;P	0.50710	0.867;0.006;0.938;0.016;0.692	B;B;B;B;B	0.43701	0.248;0.003;0.428;0.021;0.152	T	0.02837	-1.1104	10	0.48119	T	0.1	.	20.2284	0.98346	0.0:0.0:1.0:0.0	.	509;509;509;509;509	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	H	509	ENSP00000442040:R509H;ENSP00000446152:R509H;ENSP00000324857:R509H;ENSP00000374084:R509H;ENSP00000374083:R509H;ENSP00000346786:R509H;ENSP00000350770:R509H;ENSP00000374079:R509H;ENSP00000348276:R509H	ENSP00000324857:R509H	R	+	2	0	SEMA6D	45845456	1.000000	0.71417	0.995000	0.50966	0.851000	0.48451	6.736000	0.74811	2.785000	0.95823	0.650000	0.86243	CGC	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1		-14.786146	0	32	127	0	0	1	0	NM_024966	4	8.302435	97	0.039604
NIPBL	25836	broad.mit.edu	hg19	5	37064956	37064956	+	Nonsense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr5:37064956C>T	ENST00000282516.8	+	47	8876	c.8377C>T	c.(8377-8379)Cga>Tga	p.R2793*		NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2793		brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding	autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)		TCAGACTTTACGATCCCTGTA	0.363	0	55.0	58.0	57.0	5	37064956	2203	4300	6503	SO:0001587	stop_gained	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190		28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667			15146186, 15146185	Standard	NM_133433	Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.8377C>T	5.37:g.37064956C>T	ENSP00000282516:p.Arg2793*	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	C	50	16.830041	0.99873	.	.	ENSG00000164190	ENST00000282516	.	.	.	5.84	4.96	0.65561	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1816	16.0322	0.80585	0.1444:0.8556:0.0:0.0	.	.	.	.	X	2793	.	ENSP00000282516:R2793X	R	+	1	2	NIPBL	37100713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.728000	0.68531	1.425000	0.47237	-0.274000	0.10170	CGA	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1		-5.820873	0	21	97	0	0	1	0	NM_015384	3	6.506929	55	0.051724
SF3B1	23451	broad.mit.edu	hg19	2	198267483	198267483	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr2:198267483C>T	ENST00000335508.6	-	14	1965	c.1874G>A	c.(1873-1875)cGt>cAt	p.R625H		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa			nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding	NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)		TGTTGTGTTACGGACATACTC	0.438	12	95.0	92.0	93.0	2	198267483	2203	4300	6503	SO:0001583	missense	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524		10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""		9585501	Standard	XM_005246428	Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1874G>A	2.37:g.198267483C>T	ENSP00000335321:p.Arg625His	E9PCH3	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	35	5.485860	0.96323	.	.	ENSG00000115524	ENST00000335508	T	0.74421	-0.84	5.82	5.82	0.92795	Armadillo-like helical (1);Armadillo-type fold (1);	0.053241	0.64402	D	0.000001	D	0.91369	0.7277	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93329	0.6699	10	0.87932	D	0	.	20.0991	0.97865	0.0:1.0:0.0:0.0	.	625	O75533	SF3B1_HUMAN	H	625	ENSP00000335321:R625H	ENSP00000335321:R625H	R	-	2	0	SF3B1	197975728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.728000	0.84847	2.752000	0.94435	0.655000	0.94253	CGT	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		61.284105	0	2	57	0	0	1	0		20	61.406337	25	0.444444
LAMA1	284217	broad.mit.edu	hg19	18	6985237	6985237	+	Splice_Site	SNP	T	T	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr18:6985237T>A	ENST00000389658.3	-	39	5752	c.5659A>T	c.(5659-5661)Agt>Tgt	p.S1887C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1887	Domain II and I.	axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding	NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)			TGTTCCTACCTGTACAGAACA	0.493	0	181.0	149.0	160.0	18	6985237	2203	4300	6503	SO:0001630	splice_region_variant	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680	"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA	2591971	Standard	NM_005559	Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5660+1A>T	18.37:g.6985237T>A			ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480247	0.44044	.	.	ENSG00000101680	ENST00000389658	T	0.20200	2.09	4.85	3.66	0.41972	.	0.202178	0.48767	D	0.000178	T	0.35828	0.0945	L	0.56769	1.78	0.35060	D	0.761436	D	0.71674	0.998	P	0.60286	0.872	T	0.50634	-0.8805	10	0.62326	D	0.03	.	10.9662	0.47414	0.0:0.0:0.157:0.843	.	1887	P25391	LAMA1_HUMAN	C	1887	ENSP00000374309:S1887C	ENSP00000374309:S1887C	S	-	1	0	LAMA1	6975237	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	4.469000	0.60169	0.928000	0.37168	0.533000	0.62120	AGT	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1		242.333831	0	49	284	0	0	1	0	NM_005559	77	244.388304	120	0.390863
ATXN1	6310	broad.mit.edu	hg19	6	16327258	16327258	+	Silent	SNP	G	G	C			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr6:16327258G>C	ENST00000244769.4	-	8	2220	c.1284C>G	c.(1282-1284)ctC>ctG	p.L428L	ATXN1_ENST00000436367.1_Silent_p.L428L	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	428		cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association	NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)			TGTGGGGTGAGAGCGCGTAGG	0.607	0	135.0	142.0	140.0	6	16327258	2203	4300	6503	SO:0001819	synonymous_variant	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788	"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1	1582256	Standard	NM_000332	Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1284C>G	6.37:g.16327258G>C		Q17S02|Q9UJG2|Q9Y4J1	ENST00000244769.4	37	CCDS34342.1																																																																																			ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3		124.631784	0	-38	163	0	0	1	0	NM_000332	47	136.022087	145	0.244792
FAM187B	148109	broad.mit.edu	hg19	19	35719115	35719115	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr19:35719115G>A	ENST00000324675.3	-	1	517	c.469C>T	c.(469-471)Ccg>Tcg	p.P157S		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	157			integral to membrane		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9					CACTCGCCCGGCTCCTCACAG	0.607	0	66.0	66.0	66.0	19	35719115	2203	4300	6503	SO:0001583	missense	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558		26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162		Standard	NM_152481	Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.469C>T	19.37:g.35719115G>A	ENSP00000323355:p.Pro157Ser	Q8N7G6	ENST00000324675.3	37	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759151	0.49468	.	.	ENSG00000177558	ENST00000324675	T	0.22743	1.94	5.07	4.01	0.46588	.	0.811537	0.10685	N	0.645876	T	0.36963	0.0986	L	0.45581	1.43	0.09310	N	1	D	0.67145	0.996	P	0.62813	0.907	T	0.14531	-1.0469	10	0.56958	D	0.05	-12.3117	11.7034	0.51583	0.0:0.1786:0.8214:0.0	.	157	Q17R55	F187B_HUMAN	S	157	ENSP00000323355:P157S	ENSP00000323355:P157S	P	-	1	0	FAM187B	40410955	0.335000	0.24748	0.001000	0.08648	0.010000	0.07245	3.102000	0.50291	1.214000	0.43395	0.655000	0.94253	CCG	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1		68.049015	0	21	87	0	0	1	0	NM_152481	22	68.049015	22	0.500000
RTCA	8634	broad.mit.edu	hg19	1	100741270	100741270	+	Missense_Mutation	SNP	A	A	G			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr1:100741270A>G	ENST00000370128.4	+	7	900	c.731A>G	c.(730-732)aAt>aGt	p.N244S	RTCA_ENST00000260563.4_Missense_Mutation_p.N257S	NM_003729.3	NP_003720.1	O00442	RTC1_HUMAN	RNA 3'-terminal phosphate cyclase	244		RNA processing	mitochondrion|nucleoplasm	ATP binding|protein binding|RNA binding|RNA-3'-phosphate cyclase activity							GGCAATGGAAATGGAATAATG	0.363	0	94.0	97.0	96.0	1	100741270	2203	4300	6503	SO:0001583	missense	Y11651	CCDS768.1, CCDS44178.1	1p13.3	2012-03-30	2012-03-30	2012-03-30	ENSG00000137996	ENSG00000137996		17981	protein-coding gene	gene with protein product		611286	"""RTC domain containing 1"", ""RNA terminal phosphate cyclase domain 1"""	RTCD1	9184239	Standard	NM_003729	Approved	RPC, RTC1	uc001dtd.3	O00442	OTTHUMG00000010920	ENST00000370128.4:c.731A>G	1.37:g.100741270A>G	ENSP00000359146:p.Asn244Ser	Q5VVL5|Q5VVL6|Q96E99	ENST00000370128.4	37	CCDS768.1	.	.	.	.	.	.	.	.	.	.	A	0.493	-0.874326	0.02550	.	.	ENSG00000137996	ENST00000370128;ENST00000260563	.	.	.	5.23	0.354	0.16063	-terminal phosphate cyclase, subset, insert domain (2);-terminal phosphate cyclase, insert domain (1);-terminal phosphate cyclase domain (1);RNA 3&apos (5);-terminal phosphate cyclase (1);	0.190054	0.56097	N	0.000033	T	0.03827	0.0108	N	0.00256	-1.76	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29119	-1.0022	9	0.19590	T	0.45	-8.0717	7.6287	0.28226	0.3542:0.1466:0.4992:0.0	.	257;244	O00442-2;O00442	.;RTC1_HUMAN	S	244;257	.	ENSP00000260563:N257S	N	+	2	0	RTCD1	100513858	1.000000	0.71417	0.732000	0.30844	0.772000	0.43724	0.838000	0.27572	-0.181000	0.10619	-0.250000	0.11733	AAT	RTCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030098.2		127.649095	0	1	100	0	0	1	0		38	127.673728	41	0.481013
CHST15	51363	broad.mit.edu	hg19	10	125805512	125805512	+	Missense_Mutation	SNP	G	G	A	rs145631200		TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr10:125805512G>A	ENST00000346248.5	-	2	859	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C	CHST15_ENST00000421115.1_Missense_Mutation_p.R73C|CHST15_ENST00000435907.1_Missense_Mutation_p.R73C	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	73		hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity	endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26					TTTTTGAAGCGCAAAAACCCA	0.453	0	85.0	75.0	79.0	10	125805512	2203	4300	6503	SO:0001583	missense	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277			9628581, 9754571, 11572857	Standard	NM_014863	Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.217C>T	10.37:g.125805512G>A	ENSP00000333947:p.Arg73Cys	O60338|O60474|Q86VM4	ENST00000346248.5	37	CCDS7638.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.620	0.676663	0.14841	6.81E-4	0.0	ENSG00000182022	ENST00000346248;ENST00000435907;ENST00000434607;ENST00000546346;ENST00000421115	.	.	.	5.67	4.77	0.60923	.	0.253960	0.41294	N	0.000904	T	0.20740	0.0499	N	0.04508	-0.205	0.31534	N	0.660833	B;B	0.25007	0.116;0.071	B;B	0.19391	0.025;0.011	T	0.13469	-1.0508	9	0.44086	T	0.13	-28.6264	9.5674	0.39407	0.1996:0.0:0.8004:0.0	.	73;73	Q7LFX5-2;Q7LFX5	.;CHSTF_HUMAN	C	73	.	ENSP00000333947:R73C	R	-	1	0	CHST15	125795502	0.905000	0.30787	0.951000	0.38953	0.262000	0.26303	1.908000	0.39907	1.415000	0.47037	-0.219000	0.12488	CGC	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1		-10.733289	0	-12	92	0	0	1	0	NM_015892	3	6.364739	72	0.040000
SLC28A3	64078	broad.mit.edu	hg19	9	86894188	86894188	+	Silent	SNP	C	C	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr9:86894188C>A	ENST00000376238.4	-	17	1990	c.1941G>T	c.(1939-1941)ctG>ctT	p.L647L	RP11-380F14.2_ENST00000419815.1_RNA|SLC28A3_ENST00000537648.1_Silent_p.L578L	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	647		nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding	endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					ACCTGCTCAACAGACTTTGGC	0.348	0	131.0	113.0	119.0	9	86894188	2203	4300	6503	SO:0001819	synonymous_variant	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506	"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""		11032837	Standard	NM_001199633	Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1941G>T	9.37:g.86894188C>A		A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	ENST00000376238.4	37	CCDS6670.1																																																																																			SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1		58.815122	1	23	96	0	1.56452e-12	1	1.61342e-12	NM_022127	19	59.270906	29	0.395833
ZNF335	63925	broad.mit.edu	hg19	20	44579207	44579207	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr20:44579207G>A	ENST00000322927.2	-	21	3317	c.3217C>T	c.(3217-3219)Cgg>Tgg	p.R1073W	ZNF335_ENST00000426788.1_Missense_Mutation_p.R918W	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1073		regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)			TGGTGGGGCCGTAGGCTTGAG	0.582	0	132.0	143.0	140.0	20	44579207	2203	4300	6503	SO:0001583	missense	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026	"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827			12215545, 19131338	Standard	NM_022095	Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3217C>T	20.37:g.44579207G>A	ENSP00000325326:p.Arg1073Trp	B4DLG7|Q548D0|Q9H684	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.618895	0.66787	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.17854	2.25;2.25	4.82	3.85	0.44370	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.50154	0.1599	M	0.93016	3.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.63829	-0.6548	10	0.87932	D	0	-33.4049	13.4975	0.61434	0.0:0.0:0.8375:0.1625	.	918;1073	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	W	1073;850;918	ENSP00000325326:R1073W;ENSP00000397098:R918W	ENSP00000243961:R850W	R	-	1	2	ZNF335	44012614	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	4.921000	0.63397	1.341000	0.45600	0.563000	0.77884	CGG	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1		-26.823814	0	30	221	0	0	1	0	NM_022095	4	6.327960	132	0.029412
SORL1	6653	broad.mit.edu	hg19	11	121429472	121429472	+	Missense_Mutation	SNP	A	A	T			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr11:121429472A>T	ENST00000260197.7	+	20	2965	c.2836A>T	c.(2836-2838)Atc>Ttc	p.I946F		NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	946		cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity	NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)	CATAGAGCGGATCACGTTCAG	0.547	0	204.0	158.0	174.0	11	121429472	2203	4299	6502	SO:0001583	missense	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642	"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32	9157966, 8940146	Standard	NM_003105	Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.2836A>T	11.37:g.121429472A>T	ENSP00000260197:p.Ile946Phe	B2RNX7|Q92856	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535708	0.45176	.	.	ENSG00000137642	ENST00000260197	D	0.90844	-2.74	5.53	1.72	0.24424	Six-bladed beta-propeller, TolB-like (1);	0.620996	0.17025	N	0.189966	D	0.90038	0.6889	M	0.86953	2.85	0.80722	D	1	B	0.23735	0.09	B	0.23574	0.047	D	0.85774	0.1357	10	0.59425	D	0.04	.	7.8776	0.29603	0.5602:0.0:0.4398:0.0	.	946	Q92673	SORL_HUMAN	F	946	ENSP00000260197:I946F	ENSP00000260197:I946F	I	+	1	0	SORL1	120934682	0.997000	0.39634	0.058000	0.19502	0.779000	0.44077	2.240000	0.43088	0.307000	0.22880	0.533000	0.62120	ATC	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2		65.268417	0	18	93	0	0	1	0	NM_003105	24	67.298587	50	0.324324
FAM198B	51313	broad.mit.edu	hg19	4	159076823	159076823	+	Silent	SNP	A	A	G			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr4:159076823A>G	ENST00000296530.8	-	3	1686	c.1065T>C	c.(1063-1065)ggT>ggC	p.G355G	FAM198B_ENST00000585682.1_Silent_p.G355G|FAM198B_ENST00000589306.1_5'UTR|FAM198B_ENST00000393807.5_Silent_p.G363G	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	355			Golgi membrane|integral to membrane		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26					TTTCAGTACAACCCGATTCAG	0.418	0	115.0	93.0	101.0	4	159076823	2203	4299	6502	SO:0001819	synonymous_variant		CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125		25312	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 18"""	C4orf18	12975309	Standard	NM_001031700	Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.1065T>C	4.37:g.159076823A>G		Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	ENST00000296530.8	37	CCDS3798.1																																																																																			FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1		83.169119	0	-2	69	0	0	1	0	NM_001031700, NM_016613	25	83.409099	33	0.431034
TRIM15	89870	broad.mit.edu	hg19	6	30135042	30135042	+	Silent	SNP	G	G	A			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr6:30135042G>A	ENST00000376694.4	+	2	940	c.471G>A	c.(469-471)gtG>gtA	p.V157V	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	157		mesodermal cell fate determination	intracellular	zinc ion binding	large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14					AGCTTCAAGTGCTGCTGGTAC	0.502	0	116.0	97.0	104.0	6	30135042	1511	2709	4220	SO:0001819	synonymous_variant	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610	"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178	11331580, 8304341, 8812418	Standard	NM_033229	Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.471G>A	6.37:g.30135042G>A		A2BEC9|O95604|Q8IUX9|Q9C018	ENST00000376694.4	37	CCDS4677.1																																																																																			TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2		297.467262	0	-8	74	0	0	1	0	NM_033229	91	301.892533	40	0.694656
DNAJB6	10049	broad.mit.edu	hg19	7	157177640	157177656	+	Frame_Shift_Del	DEL	CAACTTCAAATCGATAT	CAACTTCAAATCGATAT	-	rs145897776		TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr7:157177640_157177656delCAACTTCAAATCGATAT	ENST00000262177.4	+	7	763_779	c.558_574delCAACTTCAAATCGATAT	c.(556-576)ggcaacttcaaatcgatatcafs	p.NFKSIS187fs	DNAJB6_ENST00000429029.2_Frame_Shift_Del_p.NFKSIS187fs|DNAJB6_ENST00000443280.1_Intron|DNAJB6_ENST00000452797.2_Frame_Shift_Del_p.NFKSIS138fs	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	187	Interaction with KRT18.	intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding	central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)	GTGGCATGGGCAACTTCAAATCGATATCAACTTCAAC	0.396	1									SO:0001589	frameshift_variant	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993	"""Heat shock proteins / DNAJ (HSP40)"""	14888	protein-coding gene	gene with protein product		611332	"""limb girdle muscular dystrophy 1D (autosomal dominant)"""	LGMD1D	10319584, 9915854, 22366786	Standard	NM_005494	Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000429029.2:c.558_574delCAACTTCAAATCGATAT	7.37:g.157177640_157177656delCAACTTCAAATCGATAT	ENSP00000397556:p.Asn187fs	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	ENST00000429029.2	37	CCDS47755.1																																																																																			DNAJB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348120.1	.	.		45	159						15		77	0.16
GNPTG	84572	broad.mit.edu	hg19	16	1402156	1402156	+	Frame_Shift_Del	DEL	T	T	-			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr16:1402156delT	ENST00000204679.4	+	2	149	c.106delT	c.(106-108)tttfs	p.F36fs		NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	36			extracellular region|Golgi apparatus	protein binding	breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)			GCCCAACGCGTTTGGGTGAGC	0.726	0	6.0	6.0	6.0	16	1402156	2122	4153	6275	SO:0001589	frameshift_variant	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581		23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27	10712439	Standard	NM_032520	Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.106delT	16.37:g.1402156delT	ENSP00000204679:p.Phe36fs	B2R556|Q6XYD7|Q96L13	ENST00000204679.4	37	CCDS10436.1																																																																																			GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	.	.		2	10					NM_032520	2		4	0.33
HGFAC	3083	broad.mit.edu	hg19	4	3446075	3446075	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WC-A885-01A-11D-A39W-08	TCGA-WC-A885-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26623935-ef1b-48ed-82be-61f510b345f1	b4aab0c3-d7a4-4363-8f30-0ffe07fdd691	g.chr4:3446075delG	ENST00000382774.3	+	6	751	c.636delG	c.(634-636)gagfs	p.E212fs	HGFAC_ENST00000511533.1_Frame_Shift_Del_p.E212fs	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	212	Fibronectin type-I.	proteolysis	extracellular space	protein binding|serine-type endopeptidase activity	central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	AGTACCTGGAGGGGGGCGACC	0.682	0	12.0	15.0	14.0	4	3446075	2170	4280	6450	SO:0001589	frameshift_variant	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758		4894	protein-coding gene	gene with protein product		604552			7683665, 8226803	Standard	XM_005247966	Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.636delG	4.37:g.3446075delG	ENSP00000372224:p.Glu212fs	Q14726|Q2M1W7|Q53X47	ENST00000382774.3	37	CCDS3369.1																																																																																			HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3	.	.		3	7						2		4	0.33