#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	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_dbSNPPopFreq	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_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
MST1L	11223	bcgsc.ca	37	1	17084768	17084768	+	RNA	SNP	G	G	C			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:17084768G>C	ENST00000455405.2	-	0	248							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TAGAGACCCCGCGCAGAAATG	0.572																																					.													.	.			0			.																																											11223	.			GACCCCGCGCAGA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084768G>C			Somatic	181	0.0110497238	2		WXS	Illumina HiSeq	Phase_1	197	0.06	12	.	2	0.00	0	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.693221	0.00731	.	.	ENSG00000186715	ENST00000389184;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.12050	0.0293	.	.	.	.	.	.	B	0.06786	0.001	B	0.08055	0.003	T	0.38308	-0.9667	5	0.02654	T	1	.	3.5811	0.07954	2.0E-4:0.4998:0.4998:2.0E-4	rs2092129;rs3982161	512	Q2TV78	MSTP9_HUMAN	G	481;512	.	ENSP00000445850:A481G	A	-	2	0	MST1P9	16957355	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	3.026000	0.49689	-0.000000	0.14550	0.000000	0.15137	GCG			0.572	MST1L-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000400328.1		NM_001271733	
XKR8	55113	broad.mit.edu	37	1	28293362	28293362	+	Missense_Mutation	SNP	G	G	A	rs147277716		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:28293362G>A	ENST00000373884.5	+	3	1447	c.839G>A	c.(838-840)cGc>cAc	p.R280H		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	280					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		GCTGAGGGCCGCACCCGAGGC	0.642																																					p.R280H													.	XKR8	15		0			c.G839A							G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	27.0	27.0	27.0		839	-9.5	0.2	1	dbSNP_134	27	0,8600		0,0,4300	no	missense	XKR8	NM_018053.2	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	280/396	28293362	2,13004	2203	4300	6503	SO:0001583	missense	55113	exon3			AGGGCCGCACCCG	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.839G>A	1.37:g.28293362G>A	ENSP00000362991:p.Arg280His		Somatic	88	0.0113636364	1		WXS	Illumina HiSeq	Phase_I	72	0.04	3	NM_018053	34	0.00	0		Missense_Mutation	SNP	ENST00000373884.5	37	CCDS315.1	.	.	.	.	.	.	.	.	.	.	G	1.796	-0.478334	0.04414	4.54E-4	0.0	ENSG00000158156	ENST00000373884	T	0.66460	-0.21	4.73	-9.46	0.00597	.	0.976052	0.08445	N	0.944882	T	0.49847	0.1581	N	0.25426	0.745	0.22266	N	0.999241	B	0.18310	0.027	B	0.14578	0.011	T	0.36578	-0.9742	10	0.27082	T	0.32	.	18.3907	0.90483	0.195:0.0862:0.7189:0.0	.	280	Q9H6D3	XKR8_HUMAN	H	280	ENSP00000362991:R280H	ENSP00000362991:R280H	R	+	2	0	XKR8	28165949	0.000000	0.05858	0.153000	0.22517	0.188000	0.23474	-1.137000	0.03219	-2.627000	0.00436	-2.769000	0.00120	CGC			0.642	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000011175.1		NM_018053	
CELF3	11189	broad.mit.edu	37	1	151678746	151678746	+	Silent	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:151678746C>T	ENST00000290583.4	-	10	1873	c.1080G>A	c.(1078-1080)caG>caA	p.Q360Q	RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000290585.4_Silent_p.Q310Q|CELF3_ENST00000392706.3_Silent_p.Q155Q	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	360	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgctgctgttgAGGTG	0.652																																					p.Q360Q													.	CELF3	49		0			c.G1080A												19.0	21.0	20.0					1																	151678746		2199	4294	6493	SO:0001819	synonymous_variant	11189	exon10			CTGCTGCTGTTGA	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1080G>A	1.37:g.151678746C>T			Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	37	0.14	5	NM_007185	1	0.00	0	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	8.446	0.851874	0.17034	.	.	ENSG00000159409	ENST00000420342	.	.	.	4.18	3.18	0.36537	.	.	.	.	.	T	0.45994	0.1370	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41910	-0.9482	4	.	.	.	-1.649	8.7523	0.34622	0.0:0.876:0.0:0.124	.	.	.	.	N	361	.	.	S	-	2	0	CELF3	149945370	.	.	1.000000	0.80357	0.943000	0.58893	.	.	2.183000	0.69458	0.655000	0.94253	AGC			0.652	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000036663.2		NM_007185	
C1orf61	10485	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156384450	156384450	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:156384450C>T	ENST00000368243.1	-	4	283	c.167G>A	c.(166-168)cGg>cAg	p.R56Q		NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	56						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					ACTCACCGCCCGGGAGCTGTC	0.557											OREG0006902	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=C1orf61|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R56Q													.	.			0			c.G167A												33.0	31.0	31.0					1																	156384450		2203	4300	6503	SO:0001583	missense	10485	exon4			ACCGCCCGGGAGC		CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"""contingent replication of cDNA-4"", ""transcriptional activator of the c fos promoter"""					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.167G>A	1.37:g.156384450C>T	ENSP00000357226:p.Arg56Gln		Somatic	60	0	0	1778	WXS	Illumina HiSeq	.	78	0.26	20	NM_006365	1	1.00	1	B1ALL5|B1ALL8	Missense_Mutation	SNP	ENST00000368243.1	37	CCDS1142.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.40|12.40	1.927213|1.927213	0.34002|0.34002	.|.	.|.	ENSG00000125462|ENSG00000125462	ENST00000368242|ENST00000310027;ENST00000368243;ENST00000357975	.|.	.|.	.|.	3.48|3.48	-6.97|-6.97	0.01616|0.01616	.|.	.|.	.|.	.|.	.|.	T|T	0.07188|0.07188	0.0182|0.0182	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B	.|0.24368	.|0.102	.|B	.|0.13407	.|0.009	T|T	0.11966|0.11966	-1.0566|-1.0566	5|8	.|0.36615	.|T	.|0.2	.|.	5.1642|5.1642	0.15077|0.15077	0.2545:0.1828:0.0:0.5628|0.2545:0.1828:0.0:0.5628	.|.	.|56	.|Q13536	.|CROC4_HUMAN	R|Q	88|70;56;69	.|.	.|ENSP00000310651:R70Q	G|R	-|-	1|2	0|0	C1orf61|C1orf61	154651074|154651074	0.000000|0.000000	0.05858|0.05858	0.016000|0.016000	0.15963|0.15963	0.984000|0.984000	0.73092|0.73092	-1.949000|-1.949000	0.01532|0.01532	-2.214000|-2.214000	0.00734|0.00734	-0.258000|-0.258000	0.10820|0.10820	GGG|CGG			0.557	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000075988.1		NM_006365	
Unknown	0	bcgsc.ca	37	1	192215884	192215884	+	IGR	SNP	C	C	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:192215884C>G								RGS18 (60939 upstream) : RGS21 (70237 downstream)																							GTTCTACATCCTTAATTGAAT	0.318																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TACATCCTTAATT																													1.37:g.192215884C>G			Somatic	299	0	0		WXS	Illumina HiSeq	Phase_1	280	0.16	46	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.318										
RP11-739N20.2	0	broad.mit.edu	37	1	204363980	204363981	+	RNA	DEL	AA	AA	-			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr1:204363980_204363981delAA	ENST00000443515.1	+	0	146																											tttgtttttcaaaaaaaaaaaa	0.307																																					.													.	.			0			.																																											0	.			TTTTTCAAAAAAA																													1.37:g.204363990_204363991delAA			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000443515.1	37																																																																																						0.307	RP11-739N20.2-001	KNOWN	basic	antisense	antisense		OTTHUMT00000087972.1			
DPCD	25911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	103361002	103361002	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr10:103361002C>T	ENST00000370151.4	+	4	362	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	MIR3158-1_ENST00000583596.1_RNA|DPCD_ENST00000370147.1_Missense_Mutation_p.R105W|DPCD_ENST00000370148.2_Missense_Mutation_p.R105W	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	105					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						TTTCCAGTGGCGGATTCGAAA	0.517																																					p.R105W													.	.			0			c.C313T												161.0	125.0	137.0					10																	103361002		2203	4300	6503	SO:0001583	missense	25911	exon4			CAGTGGCGGATTC		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.313C>T	10.37:g.103361002C>T	ENSP00000359170:p.Arg105Trp		Somatic	69	0	0		WXS	Illumina HiSeq	.	80	0.23	18	NM_015448	30	0.37	11	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	37	CCDS7514.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.039223	0.75617	.	.	ENSG00000166171	ENST00000370151;ENST00000370147;ENST00000370148;ENST00000370149;ENST00000434727	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	5.95	4.09	0.47781	.	0.000000	0.85682	D	0.000000	T	0.75042	0.3796	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77225	-0.2666	10	0.87932	D	0	-13.8538	8.7911	0.34852	0.2693:0.663:0.0:0.0677	.	105	Q9BVM2	DPCD_HUMAN	W	105;105;105;70;69	ENSP00000359170:R105W;ENSP00000359166:R105W;ENSP00000359167:R105W;ENSP00000403505:R69W	ENSP00000359166:R105W	R	+	1	2	DPCD	103350992	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.506000	0.53364	0.843000	0.35070	0.650000	0.86243	CGG			0.517	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049958.2			
MUC2	4583	broad.mit.edu	37	11	1093292	1093292	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr11:1093292C>T	ENST00000441003.2	+	30	5138	c.5111C>T	c.(5110-5112)aCc>aTc	p.T1704I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1671I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	atcaccaccaccactacggtg	0.637																																					p.T1704I													.	MUC2	614		0			c.C5111T												107.0	156.0	138.0					11																	1093292		1878	3453	5331	SO:0001583	missense	4583	exon30			CCACCACCACTAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5111C>T	11.37:g.1093292C>T	ENSP00000415183:p.Thr1704Ile		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	0.17	3	NM_002457	0		0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.150	-0.394632	0.04899	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11063	2.81;2.84	1.6	-2.66	0.06077	.	2.760050	0.04005	U	0.297091	T	0.06416	0.0165	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.36286	-0.9754	9	0.36615	T	0.2	.	2.477	0.04578	0.4942:0.3128:0.0:0.1931	.	1704	E7EUV1	.	I	1704;1671	ENSP00000415183:T1704I;ENSP00000351956:T1671I	ENSP00000351956:T1671I	T	+	2	0	MUC2	1083292	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.330000	0.19715	-0.514000	0.06488	0.184000	0.17185	ACC			0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000345894.2		NM_002457	
SLC43A3	29015	bcgsc.ca	37	11	57193118	57193118	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr11:57193118G>T	ENST00000395123.2	-	4	514	c.210C>A	c.(208-210)ttC>ttA	p.F70L	SLC43A3_ENST00000352187.1_Missense_Mutation_p.F70L|SLC43A3_ENST00000529554.1_Missense_Mutation_p.F70L|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000395124.1_Missense_Mutation_p.F70L|SLC43A3_ENST00000533524.1_Missense_Mutation_p.F83L	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	70					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						AGATGAGTGAGAACCTCTCAT	0.542																																					p.F70L													.	SLC43A3	54		0			c.C210A												104.0	93.0	97.0					11																	57193118		2201	4296	6497	SO:0001583	missense	29015	exon4			GAGTGAGAACCTC	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"""Solute carriers"""	17466	protein-coding gene	gene with protein product	"""likely ortholog of mouse embryonic epithelial gene 1"""					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.210C>A	11.37:g.57193118G>T	ENSP00000378555:p.Phe70Leu		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_1	84	0.06	5	NM_014096	5	0.00	0	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	G	2.613	-0.290285	0.05568	.	.	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005;ENST00000529113;ENST00000525474;ENST00000529112;ENST00000528187;ENST00000529494;ENST00000533245;ENST00000533235;ENST00000524863;ENST00000532795;ENST00000533051	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.13307	2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6	5.4	4.49	0.54785	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.08133	0.0203	N	0.17631	0.505	0.49130	D	0.999753	P;B;B	0.38420	0.63;0.091;0.047	B;B;B	0.40285	0.325;0.149;0.066	T	0.12192	-1.0557	10	0.02654	T	1	-32.7492	9.246	0.37527	0.1673:0.0:0.8327:0.0	.	70;83;70	B4DV87;E7EQD2;Q8NBI5	.;.;S43A3_HUMAN	L	70;70;70;70;83;70;17;70;70;83;70;70;70;70;70;70	ENSP00000378555:F70L;ENSP00000378556:F70L;ENSP00000337561:F70L;ENSP00000436254:F70L;ENSP00000434515:F83L;ENSP00000435893:F70L;ENSP00000434293:F17L;ENSP00000436055:F70L;ENSP00000434913:F70L;ENSP00000435273:F83L;ENSP00000433974:F70L;ENSP00000431762:F70L;ENSP00000435156:F70L;ENSP00000434569:F70L;ENSP00000435109:F70L;ENSP00000435490:F70L	ENSP00000337561:F70L	F	-	3	2	SLC43A3	56949694	1.000000	0.71417	0.954000	0.39281	0.221000	0.24807	1.864000	0.39469	1.272000	0.44329	0.561000	0.74099	TTC			0.542	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000393057.1		NM_017611	
IQSEC3	440073	hgsc.bcm.edu	37	12	274692	274692	+	Missense_Mutation	SNP	G	G	C			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr12:274692G>C	ENST00000538872.1	+	10	2920	c.2802G>C	c.(2800-2802)gaG>gaC	p.E934D	RP11-598F7.5_ENST00000540136.1_RNA|IQSEC3_ENST00000326261.4_Missense_Mutation_p.E934D|RP11-598F7.6_ENST00000537295.1_lincRNA|IQSEC3_ENST00000382841.2_Missense_Mutation_p.E631D			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	934	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AGCTCTTTGAGAACGAGTGTA	0.498																																					p.E934D													.	.			0			c.G2802C												143.0	133.0	137.0					12																	274692		2203	4300	6503	SO:0001583	missense	440073	exon10			CTTTGAGAACGAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2802G>C	12.37:g.274692G>C	ENSP00000437554:p.Glu934Asp		Somatic	87	0	0		WXS	Illumina HiSeq	.	253	0.04	11	NM_001170738	4	0.00	0	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	37	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594755	0.66219	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.52057	0.68;0.68;0.68	4.87	4.87	0.63330	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.69185	2.1	0.80722	D	1	B;B	0.16603	0.002;0.018	B;B	0.17098	0.012;0.017	T	0.49312	-0.8953	10	0.45353	T	0.12	.	18.5623	0.91105	0.0:0.0:1.0:0.0	.	934;631	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	D	934;934;631	ENSP00000437554:E934D;ENSP00000315662:E934D;ENSP00000372292:E631D	ENSP00000315662:E934D	E	+	3	2	IQSEC3	144953	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.377000	0.66184	2.684000	0.91462	0.650000	0.86243	GAG			0.498	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000397382.3		XM_495902	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244878	11244878	+	5'UTR	SNP	A	A	G	rs369719862		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr12:11244878A>G	ENST00000531678.1	-	0	34				TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43						detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		tgtgtccggaattggttcctg	0.433																																					.													.	.			0			.												4.0	3.0	4.0					12																	11244878		847	1536	2383	SO:0001623	5_prime_UTR_variant	259289	.			TCCGGAATTGGTT	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.-50T>C	12.37:g.11244878A>G			Somatic	18	0	0		WXS	Illumina HiSeq	.	93	0.06	6	.	0		0	P59546|Q645X4	RNA	SNP	ENST00000531678.1	37	CCDS53749.1																																																																																					0.433	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000383561.1		NM_176884	
FAM186A	121006	broad.mit.edu	37	12	50756999	50756999	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr12:50756999G>T	ENST00000327337.5	-	2	340	c.341C>A	c.(340-342)gCt>gAt	p.A114D	FAM186A_ENST00000543111.1_Missense_Mutation_p.A114D	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	114																	AGCGTAAGTAGCCATTTTCTC	0.383																																					p.A114D	NSCLC(138;1796 1887 12511 19463 37884)												.	FAM186A	181		0			c.C341A												207.0	176.0	186.0					12																	50756999		692	1591	2283	SO:0001583	missense	121006	exon2			TAAGTAGCCATTT		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.341C>A	12.37:g.50756999G>T	ENSP00000329995:p.Ala114Asp		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	108	0.04	4	NM_001145475	0		0		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757831	0.49468	.	.	ENSG00000185958	ENST00000543111;ENST00000327337	T;T	0.13538	2.58;2.58	4.12	-5.02	0.02982	.	.	.	.	.	T	0.11750	0.0286	L	0.49126	1.545	0.09310	N	1	P	0.49635	0.926	P	0.44447	0.45	T	0.13124	-1.0521	9	0.87932	D	0	.	4.0376	0.09737	0.3877:0.0:0.3237:0.2886	.	114	A6NE01	F186A_HUMAN	D	114	ENSP00000441337:A114D;ENSP00000329995:A114D	ENSP00000329995:A114D	A	-	2	0	FAM186A	49043266	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.294000	0.08309	-0.672000	0.05266	-0.310000	0.09108	GCT			0.383	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000396838.1		XM_001718353	
ITGA7	3679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	56092570	56092570	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr12:56092570C>T	ENST00000555728.1	-	7	1082	c.1054G>A	c.(1054-1056)Gag>Aag	p.E352K	ITGA7_ENST00000553804.1_Missense_Mutation_p.E312K|ITGA7_ENST00000394230.2_Missense_Mutation_p.E312K|ITGA7_ENST00000394229.2_Missense_Mutation_p.E308K|ITGA7_ENST00000347027.6_Missense_Mutation_p.E308K|ITGA7_ENST00000257879.6_Missense_Mutation_p.E308K|ITGA7_ENST00000257880.7_Missense_Mutation_p.E352K|ITGA7_ENST00000452168.2_Missense_Mutation_p.E215K			Q13683	ITA7_HUMAN	integrin, alpha 7	352					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AGCATAACCTCGGGCACCAGG	0.642																																					p.E312K													ITGA7_ENST00000553804,colon,carcinoma,0,2	ITGA7_ENST00000553804	0	2	0			c.G934A												65.0	53.0	57.0					12																	56092570		2203	4300	6503	SO:0001583	missense	3679	exon6			TAACCTCGGGCAC		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.1054G>A	12.37:g.56092570C>T	ENSP00000452387:p.Glu352Lys		Somatic	92	0	0		WXS	Illumina HiSeq	.	100	0.25	25	NM_001144996	9	0.22	2	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	37		.	.	.	.	.	.	.	.	.	.	C	14.16	2.453407	0.43531	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728;ENST00000557257	T;T;T;T;T;T;T;T;T	0.68903	-0.32;-0.34;-0.28;0.13;-0.35;-0.32;-0.34;-0.36;1.38	4.46	4.46	0.54185	.	0.304228	0.30602	N	0.009277	T	0.53546	0.1803	N	0.21448	0.665	0.43657	D	0.996072	B;B;P;B	0.34757	0.043;0.025;0.467;0.049	B;B;B;B	0.36808	0.052;0.014;0.233;0.027	T	0.52779	-0.8530	10	0.27082	T	0.32	.	14.9993	0.71459	0.0:1.0:0.0:0.0	.	215;352;312;371	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	K	312;308;308;215;352;312;308;352;352;150	ENSP00000452120:E312K;ENSP00000257879:E308K;ENSP00000343009:E308K;ENSP00000393844:E215K;ENSP00000257880:E352K;ENSP00000377777:E312K;ENSP00000377776:E308K;ENSP00000452387:E352K;ENSP00000450578:E150K	ENSP00000257879:E308K	E	-	1	0	ITGA7	54378837	1.000000	0.71417	0.474000	0.27266	0.507000	0.33981	3.974000	0.56852	2.489000	0.83994	0.491000	0.48974	GAG			0.642	ITGA7-014	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000410138.1		NM_002206	
PABPC3	5042	bcgsc.ca	37	13	25671122	25671122	+	Silent	SNP	C	C	T	rs79072440		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr13:25671122C>T	ENST00000281589.3	+	1	823	c.786C>T	c.(784-786)taC>taT	p.Y262Y		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	262	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AACAAATTTACGTTGGTCGAG	0.408																																					p.Y262Y													.	PABPC3	129		0			c.C786T																																									SO:0001819	synonymous_variant	5042	exon1			AATTTACGTTGGT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.786C>T	13.37:g.25671122C>T			Somatic	104	0.0096153846	1		WXS	Illumina HiSeq	Phase_1	103	0.08	8	NM_030979	3	1.00	3	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																					0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000044220.2		NM_030979	
POTEG	404785	broad.mit.edu	37	14	19553528	19553528	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr14:19553528A>G	ENST00000409832.3	+	1	164	c.112A>G	c.(112-114)Agc>Ggc	p.S38G		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	38										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GTGCAGGGGGAGCGGCAAGAG	0.597																																					p.S38G													.	POTEG	118		0			c.A112G												18.0	29.0	26.0					14																	19553528		1570	3325	4895	SO:0001583	missense	404785	exon1			AGGGGGAGCGGCA		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.112A>G	14.37:g.19553528A>G	ENSP00000386971:p.Ser38Gly		Somatic	988	0.0020242915	2		WXS	Illumina HiSeq	Phase_I	1024	0.01	11	NM_001005356	0		0	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	a	9.324	1.058695	0.19987	.	.	ENSG00000222036	ENST00000409832	T	0.37235	1.21	.	.	.	.	.	.	.	.	T	0.25044	0.0608	L	0.29908	0.895	0.09310	N	1	B	0.32031	0.352	B	0.34242	0.178	T	0.25916	-1.0118	7	0.72032	D	0.01	.	.	.	.	.	38	Q6S5H5	POTEG_HUMAN	G	38	ENSP00000386971:S38G	ENSP00000386971:S38G	S	+	1	0	POTEG	18623528	0.007000	0.16637	0.016000	0.15963	0.017000	0.09413	0.222000	0.17699	0.141000	0.18875	0.139000	0.15985	AGC			0.597	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000408579.1		NM_001005356	
BMS1P18	414763	broad.mit.edu	37	14	19890158	19890160	+	lincRNA	DEL	GCC	GCC	-	rs112695101|rs149570903	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	GCC	GCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr14:19890158_19890160delGCC	ENST00000552602.1	-	0	293																											GGCAGCAGCGGCCGCCAAGCATG	0.729														1183	0.236222	0.1051	0.3415	5008	,	,		25129	0.3323		0.1769	False		,,,				2504	0.3006				.													.	.			0			.																																											0	.			GCAGCGGCCGCCA																													14.37:g.19890161_19890163delGCC			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	0.80	8	.	0		0		RNA	DEL	ENST00000552602.1	37																																																																																						0.729	CTD-2314B22.3-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000409412.1			
UNC79	57578	broad.mit.edu	37	14	94103583	94103583	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr14:94103583G>T	ENST00000393151.2	+	33	5855	c.5855G>T	c.(5854-5856)cGc>cTc	p.R1952L	UNC79_ENST00000256339.4_Missense_Mutation_p.R1775L|UNC79_ENST00000555664.1_Missense_Mutation_p.R1913L|UNC79_ENST00000553484.1_Missense_Mutation_p.R1974L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1952					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						cctgggaaacgccagtgtaac	0.453																																					p.R1775L													.	UNC79	366		0			c.G5324T												154.0	116.0	129.0					14																	94103583		2203	4300	6503	SO:0001583	missense	57578	exon33			GGAAACGCCAGTG	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5855G>T	14.37:g.94103583G>T	ENSP00000376858:p.Arg1952Leu		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	0.05	4	NM_020818	0		0	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	G	15.38	2.817600	0.50633	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.21932	2.26;1.98;2.26;2.26	5.34	4.44	0.53790	.	0.406174	0.28036	N	0.016847	T	0.11495	0.0280	N	0.08118	0	0.31543	N	0.659719	B	0.13594	0.008	B	0.16289	0.015	T	0.06356	-1.0831	10	0.35671	T	0.21	-1.554	12.2277	0.54470	0.0:0.1706:0.8293:0.0	.	1974	C9JQL1	.	L	1775;1913;1974;1952;1974	ENSP00000256339:R1775L;ENSP00000450868:R1913L;ENSP00000451360:R1974L;ENSP00000376858:R1952L	ENSP00000256339:R1775L	R	+	2	0	KIAA1409	93173336	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.832000	0.48152	1.600000	0.50102	0.650000	0.86243	CGC			0.453	UNC79-006	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000412766.1		XM_028395	
GOLGA6L2	283685	bcgsc.ca	37	15	23685728	23685728	+	Missense_Mutation	SNP	C	C	G	rs376316505		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr15:23685728C>G	ENST00000567107.1	-	8	1946	c.1894G>C	c.(1894-1896)Gat>Cat	p.D632H	GOLGA6L2_ENST00000345070.5_Intron|GOLGA6L2_ENST00000312015.5_Intron			Q8N9W4	GG6L2_HUMAN	golgin A6 family-like 2	0										breast(1)|endometrium(7)	8						gctcccgcatcctctcctcct	0.592																																					.													.	.			0			.																																									SO:0001583	missense	283685	.			CCGCATCCTCTCC	AK093463		15q11.2	2012-10-05	2010-02-12		ENSG00000174450	ENSG00000174450			26695	protein-coding gene	gene with protein product	"""cancer/testis antigen 105"""		"""golgi autoantigen, golgin subfamily a, 6-like 2"""				Standard	XM_002343322		Approved	CT105, FLJ36144	uc021sfy.1	Q8N9W4	OTTHUMG00000176417	ENST00000567107.1:c.1894G>C	15.37:g.23685728C>G	ENSP00000454407:p.Asp632His		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_1	15	0.33	5	.	0		0	A1L301	Missense_Mutation	SNP	ENST00000567107.1	37																																																																																						0.592	GOLGA6L2-002	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding		OTTHUMT00000431937.1		NM_182561	
MAGEL2	54551	bcgsc.ca	37	15	23889164	23889164	+	Silent	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr15:23889164G>T	ENST00000532292.1	-	1	2011	c.1917C>A	c.(1915-1917)ccC>ccA	p.P639P		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	522					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		GCCTGCTGGTGGGGCCGTGGG	0.592																																					p.P1242P													.	MAGEL2	108		0			c.C3726A												31.0	35.0	34.0					15																	23889164		2039	4186	6225	SO:0001819	synonymous_variant	54551	exon1			GCTGGTGGGGCCG	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1917C>A	15.37:g.23889164G>T			Somatic	77	0	0		WXS	Illumina HiSeq	Phase_1	55	0.09	5	NM_019066	13	0.00	0		Silent	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	G	2.154	-0.393786	0.04899	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.28	2.39	0.29439	.	.	.	.	.	T	0.60077	0.2241	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59621	-0.7420	5	0.66056	D	0.02	.	5.5198	0.16925	0.1007:0.0:0.7046:0.1947	.	.	.	.	Q	671	.	ENSP00000433433:P671Q	P	-	2	0	MAGEL2	21440257	0.978000	0.34361	0.988000	0.46212	0.036000	0.12997	0.938000	0.28965	0.744000	0.32741	-0.244000	0.11960	CCA			0.592	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000395182.2		NM_019066	
WASH3P	374666	hgsc.bcm.edu	37	15	102515335	102515335	+	RNA	SNP	C	C	G	rs201001946		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr15:102515335C>G	ENST00000557932.1	+	0	1181				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.L386V(3)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						GGAGCGAAAGCTGGAGAAGAA	0.652																																					.													WASH3P,NS,carcinoma,0,4	WASH3P	0	4	3	Substitution - Missense(3)	prostate(2)|kidney(1)	.																																											374666	.			CGAAAGCTGGAGA			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515335C>G			Somatic	47	0	0		WXS	Illumina HiSeq	.	41	0.07	3	.	169	0.09	16		RNA	SNP	ENST00000557932.1	37		.	.	.	.	.	.	.	.	.	.	c	1.538	-0.542507	0.04053	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.125321	0.53938	D	0.000056	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-11.5249	7.9382	0.29941	0.0:1.0:0.0:0.0	.	.	.	.	V	395;386	.	.	L	+	1	2	WASH3P	100332858	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	1.146000	0.31589	0.863000	0.35553	0.184000	0.17185	CTG			0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000417608.1		NM_199163	
UBALD1	124402	broad.mit.edu	37	16	4659850	4659850	+	Silent	SNP	T	T	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr16:4659850T>G	ENST00000283474.7	-	3	446	c.318A>C	c.(316-318)tcA>tcC	p.S106S	UBALD1_ENST00000587649.1_3'UTR|UBALD1_ENST00000591897.1_Silent_p.S46S|UBALD1_ENST00000590965.1_3'UTR|UBALD1_ENST00000590891.1_Silent_p.S141S|UBALD1_ENST00000587615.1_Silent_p.S81S|UBALD1_ENST00000591401.1_Silent_p.S85S	NM_145253.2	NP_660296.1	Q8TB05	UBAD1_HUMAN	UBA-like domain containing 1	106																	GTGGCGGGGGTGACGTGGCTG	0.716																																					p.S106S													.	.			0			c.A318C												6.0	7.0	7.0					16																	4659850		2008	3990	5998	SO:0001819	synonymous_variant	124402	exon3			CGGGGGTGACGTG	BC025327	CCDS10518.1	16p13.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000153443	ENSG00000153443			29576	protein-coding gene	gene with protein product			"""family with sequence similarity 100, member A"""	FAM100A			Standard	NM_145253		Approved		uc002cwx.2	Q8TB05	OTTHUMG00000129472	ENST00000283474.7:c.318A>C	16.37:g.4659850T>G			Somatic	33	0.3636363636	12		WXS	Illumina HiSeq	Phase_I	34	0.53	18	NM_145253	27	0.44	12	Q71MF6	Silent	SNP	ENST00000283474.7	37	CCDS10518.1																																																																																					0.716	UBALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251635.2		NM_145253	
CDR2	1039	broad.mit.edu	37	16	22448752	22448753	+	5'Flank	INS	-	-	GCGGCGGCG			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr16:22448752_22448753insGCGGCGGCG	ENST00000569045.1	-	0	0				RRN3P3_ENST00000551766.1_RNA			Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa							cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GTCTCGGCTGAGCGGCGGCGGC	0.733																																					.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			CGGCTGAGCGGCG	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"""Yo paraneoplastic antigen"""	117340	"""cerebellar degeneration-related protein (62kD)"""			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850			16.37:g.22448753_22448761dupGCGGCGGCG	Exception_encountered		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	8	0.38	3	.	1	0.00	0	A8K8A8|Q13977	RNA	INS	ENST00000569045.1	37																																																																																						0.733	CDR2-006	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000430087.1			
PRPF8	10594	hgsc.bcm.edu	37	17	1579989	1579989	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr17:1579989G>T	ENST00000572621.1	-	15	2463	c.2198C>A	c.(2197-2199)aCg>aAg	p.T733K	PRPF8_ENST00000304992.6_Missense_Mutation_p.T733K			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	733					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CTCTATGGGCGTCGGCAGCCC	0.567																																					p.T733K													.	.			0			c.C2198A												135.0	139.0	138.0					17																	1579989		2203	4300	6503	SO:0001583	missense	10594	exon16			ATGGGCGTCGGCA	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2198C>A	17.37:g.1579989G>T	ENSP00000460348:p.Thr733Lys		Somatic	72	0	0		WXS	Illumina HiSeq	.	57	0.07	4	NM_006445	20	0.00	0	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788258	0.49997	.	.	ENSG00000174231	ENST00000304992	T	0.79033	-1.23	6.07	6.07	0.98685	PROCN (1);	0.000000	0.85682	D	0.000000	T	0.64527	0.2606	L	0.29908	0.895	0.80722	D	1	B	0.31256	0.316	B	0.30179	0.112	T	0.60454	-0.7260	10	0.08599	T	0.76	0.0162	13.7909	0.63140	0.0695:0.0:0.9305:0.0	.	733	Q6P2Q9	PRP8_HUMAN	K	733	ENSP00000304350:T733K	ENSP00000304350:T733K	T	-	2	0	PRPF8	1526739	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	8.029000	0.88807	2.884000	0.98904	0.655000	0.94253	ACG			0.567	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000438412.2			
KRT32	3882	hgsc.bcm.edu;bcgsc.ca	37	17	39619137	39619137	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr17:39619137G>A	ENST00000225899.3	-	6	1265	c.1162C>T	c.(1162-1164)Cgg>Tgg	p.R388W		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	388	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				CCCTCCAGCCGGGCCCGGACG	0.637																																					p.R388W													.	.			0			c.C1162T												76.0	76.0	76.0					17																	39619137		2203	4300	6503	SO:0001583	missense	3882	exon6			CCAGCCGGGCCCG	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1162C>T	17.37:g.39619137G>A	ENSP00000225899:p.Arg388Trp		Somatic	78	0	0		WXS	Illumina HiSeq	.	96	0.05	5	NM_002278	0		0		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759276	0.69763	.	.	ENSG00000108759	ENST00000225899	D	0.90004	-2.6	5.07	4.08	0.47627	Filament (1);	0.000000	0.36409	N	0.002614	D	0.96364	0.8814	H	0.97365	3.99	0.39645	D	0.97037	D	0.89917	1.0	D	0.97110	1.0	D	0.98006	1.0363	10	0.87932	D	0	.	14.0467	0.64708	0.0:0.0:0.8479:0.1521	.	388	Q14532	K1H2_HUMAN	W	388	ENSP00000225899:R388W	ENSP00000225899:R388W	R	-	1	2	KRT32	36872663	0.998000	0.40836	0.993000	0.49108	0.844000	0.47949	3.571000	0.53841	1.203000	0.43233	0.561000	0.74099	CGG			0.637	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257293.1		NM_002278	
ACE	1636	bcgsc.ca	37	17	61557201	61557201	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr17:61557201G>T	ENST00000290866.4	+	4	607	c.583G>T	c.(583-585)Gct>Tct	p.A195S	ACE_ENST00000538928.1_Missense_Mutation_p.A195S|ACE_ENST00000584529.1_3'UTR|ACE_ENST00000428043.1_Missense_Mutation_p.A195S	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	195	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CTGGCACAACGCTGCGGGCAT	0.607																																					p.A195S													ACE,NS,carcinoma,-1,1	ACE	187	1	0			c.G583T												106.0	76.0	86.0					17																	61557201		2203	4300	6503	SO:0001583	missense	1636	exon4			CACAACGCTGCGG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.583G>T	17.37:g.61557201G>T	ENSP00000290866:p.Ala195Ser		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_1	55	0.07	4	NM_000789	6	0.00	0	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	G	6.521	0.464316	0.12402	.	.	ENSG00000159640	ENST00000538928;ENST00000290866;ENST00000428043	T;T;T	0.35236	1.32;1.32;1.32	3.88	0.697	0.18081	.	0.426470	0.24357	N	0.039222	T	0.24470	0.0593	L	0.35542	1.07	0.09310	N	0.999998	B;B;B	0.30709	0.038;0.005;0.291	B;B;B	0.37731	0.06;0.027;0.257	T	0.12760	-1.0535	10	0.29301	T	0.29	-3.5288	3.7568	0.08588	0.2571:0.0:0.4713:0.2716	.	195;195;195	F5H1K1;P12821-2;P12821	.;.;ACE_HUMAN	S	195	ENSP00000439591:A195S;ENSP00000290866:A195S;ENSP00000397593:A195S	ENSP00000290866:A195S	A	+	1	0	ACE	58910933	0.056000	0.20664	0.022000	0.16811	0.092000	0.18411	1.224000	0.32539	0.329000	0.23460	-0.258000	0.10820	GCT			0.607	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000337675.2			
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	21427447	21427480	+	Frame_Shift_Del	DEL	CCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	CCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	-	rs544156623|rs372275318|rs367562646|rs564044139	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	CCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	CCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr18:21427447_21427480delCCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	ENST00000313654.9	+	32	4192_4225	c.3951_3984delCCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	c.(3949-3984)cgcctttgtgaagagatgacggggcagtgccgctgcfs	p.RLCEEMTGQCRC1317fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.RLCEEMTGQCRC1317fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1317	Domain III B.|Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGGTCGGCGCCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGCCCTCCCCGCA	0.624																																					p.1317_1328del													.	.			0			c.3950_3983del																																									SO:0001589	frameshift_variant	3909	exon32			TCGGCGCCTTTGT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3951_3984delCCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	18.37:g.21427447_21427480delCCTTTGTGAAGAGATGACGGGGCAGTGCCGCTGC	ENSP00000324532:p.Arg1317fs		Somatic	23	0	0		WXS	Illumina HiSeq	.	26	0.27	7	NM_198129	0		0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	37	CCDS42419.1																																																																																					0.624	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254824.3		NM_000227, NM_198129	
RYR1	6261	hgsc.bcm.edu	37	19	38986924	38986924	+	Silent	SNP	G	G	T	rs370261565		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr19:38986924G>T	ENST00000359596.3	+	40	6618	c.6618G>T	c.(6616-6618)acG>acT	p.T2206T	RYR1_ENST00000355481.4_Silent_p.T2206T|RYR1_ENST00000360985.3_Silent_p.T2206T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2206	6 X approximate repeats.		T -> M (in MHS1; induces an increase sensitivity to caffeine; dbSNP:rs28934000). {ECO:0000269|PubMed:11575529, ECO:0000269|PubMed:12059893, ECO:0000269|PubMed:12208234, ECO:0000269|PubMed:15448513, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:9497245}.|T -> R (in MHS1). {ECO:0000269|PubMed:16163667}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGCACGAGACGGTCATGGAGG	0.632																																					p.T2206T													RYR1,NS,carcinoma,0,1	RYR1	0	1	0			c.G6618T												115.0	94.0	101.0					19																	38986924		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon40			CGAGACGGTCATG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6618G>T	19.37:g.38986924G>T			Somatic	33	0	0		WXS	Illumina HiSeq	.	42	0.05	2	NM_001042723	0		0	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																					0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000462137.1			
SNRNP200	23020	hgsc.bcm.edu;bcgsc.ca	37	2	96943998	96943998	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr2:96943998G>T	ENST00000323853.5	-	39	5664	c.5587C>A	c.(5587-5589)Cat>Aat	p.H1863N	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1863	SEC63 2.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TTGTCTTCATGGTGCCGGATG	0.537																																					p.H1863N													.	.			0			c.C5587A												195.0	164.0	175.0					2																	96943998		2203	4300	6503	SO:0001583	missense	23020	exon39			CTTCATGGTGCCG	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5587C>A	2.37:g.96943998G>T	ENSP00000317123:p.His1863Asn		Somatic	79	0	0		WXS	Illumina HiSeq	.	93	0.06	6	NM_014014	261	0.00	0	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323663	0.60634	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	T	0.56275	0.47	5.24	5.24	0.73138	Sec63 domain (3);	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.37800	1.135	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23048	-1.0199	10	0.36615	T	0.2	-17.0802	16.7058	0.85371	0.0:0.0:1.0:0.0	.	1863	O75643	U520_HUMAN	N	1863;322;446	ENSP00000317123:H1863N	ENSP00000317123:H1863N	H	-	1	0	SNRNP200	96307725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.244000	0.95423	2.884000	0.98904	0.655000	0.94253	CAT			0.537	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252846.2		NM_014014	
ANKRD36B	57730	broad.mit.edu	37	2	98192550	98192550	+	RNA	DEL	T	T	-	rs370632971|rs67020980		TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr2:98192550delT	ENST00000443455.1	-	0	874							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CATGTGACTATTAAAAAAATA	0.184																																					.													.	.			0			.																																											57730	.			TGACTATTAAAAA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98192550delT			Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	13	0.31	4	.	0		0	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	RNA	DEL	ENST00000443455.1	37																																																																																						0.184	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000328967.2		NM_025190	
POLR1B	84172	broad.mit.edu	37	2	113333030	113333030	+	Silent	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr2:113333030G>T	ENST00000263331.5	+	15	3712	c.3132G>T	c.(3130-3132)gcG>gcT	p.A1044A	POLR1B_ENST00000417433.2_Silent_p.A988A|POLR1B_ENST00000541869.1_Silent_p.A1082A|POLR1B_ENST00000537335.1_Silent_p.A833A|POLR1B_ENST00000409894.3_Silent_p.A861A	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	1044					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						AACGGGATGCGCTTTTAGCTC	0.512																																					p.A1044A	Ovarian(16;256 576 9537 23969 41147)												POLR1B,NS,carcinoma,0,1	POLR1B	95	1	0			c.G3132T												178.0	176.0	177.0					2																	113333030		2203	4300	6503	SO:0001819	synonymous_variant	84172	exon15			GGATGCGCTTTTA	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.3132G>T	2.37:g.113333030G>T			Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	169	0.02	4	NM_019014	34	0.00	0	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Silent	SNP	ENST00000263331.5	37	CCDS2097.1																																																																																					0.512	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254083.1		NM_019014	
GAL3ST2	64090	hgsc.bcm.edu;broad.mit.edu	37	2	242742846	242742846	+	Nonsense_Mutation	SNP	C	C	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr2:242742846C>G	ENST00000192314.6	+	4	593	c.462C>G	c.(460-462)taC>taG	p.Y154*	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	154					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TCATCTACTACAAAACCTACG	0.617																																					p.Y154X													.	.			0			c.C462G												40.0	39.0	40.0					2																	242742846		2203	4299	6502	SO:0001587	stop_gained	64090	exon4			CTACTACAAAACC	AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.462C>G	2.37:g.242742846C>G	ENSP00000192314:p.Tyr154*		Somatic	131	0	0		WXS	Illumina HiSeq	.	181	0.22	39	NM_022134	0		0	Q17RK0|Q57Z52	Nonsense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.850854	0.91277	.	.	ENSG00000154252	ENST00000192314	.	.	.	4.35	3.46	0.39613	.	0.247666	0.28683	N	0.014490	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.9883	11.4695	0.50259	0.0:0.9092:0.0:0.0907	.	.	.	.	X	154	.	ENSP00000192314:Y154X	Y	+	3	2	GAL3ST2	242391519	0.522000	0.26266	0.807000	0.32361	0.572000	0.35998	0.891000	0.28309	0.929000	0.37192	0.449000	0.29647	TAC			0.617	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322792.1		NM_022134	
ELMO2	63916	hgsc.bcm.edu	37	20	45014804	45014804	+	Silent	SNP	G	G	A	rs201990540	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr20:45014804G>A	ENST00000290246.6	-	9	830	c.636C>T	c.(634-636)gcC>gcT	p.A212A	ELMO2_ENST00000372176.1_Silent_p.A124A|ELMO2_ENST00000439931.2_Silent_p.A212A|ELMO2_ENST00000396391.1_Silent_p.A212A|ELMO2_ENST00000352077.2_Silent_p.A210A|ELMO2_ENST00000445496.2_Silent_p.A29A|ELMO2_ENST00000488853.1_5'UTR	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	212					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TGATTTCCTCGGCTATCTTCT	0.527													g|||	3	0.000599042	0.0015	0.0014	5008	,	,		19968	0.0		0.0	False		,,,				2504	0.0				p.A212A													ELMO2,NS,carcinoma,-1,1	ELMO2	-1	1	0			c.C636T												135.0	124.0	128.0					20																	45014804		2203	4300	6503	SO:0001819	synonymous_variant	63916	exon8			TTCCTCGGCTATC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.636C>T	20.37:g.45014804G>A			Somatic	43	0.023255814	1		WXS	Illumina HiSeq	.	64	0.08	5	NM_182764	4	0.00	0	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			0.002		0.527	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000080466.1		NM_022086	
BCRP7	100133163	broad.mit.edu	37	22	18846121	18846121	+	3'UTR	SNP	C	C	T	rs4302302	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr22:18846121C>T	ENST00000412938.1	+	0	3479																											CACGCACTGGCGCACGATGTA	0.617																																					.													.	.			0			.																																									SO:0001624	3_prime_UTR_variant	0	.			CACTGGCGCACGA																												ENST00000412938.1:c.*3476C>T	22.37:g.18846121C>T			Somatic	106	0.0094339623	1		WXS	Illumina HiSeq	Phase_I	199	0.07	13	.	1	0.00	0		RNA	SNP	ENST00000412938.1	37																																																																																						0.617	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000471615.1			
CELSR1	9620	ucsc.edu	37	22	46768831	46768831	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr22:46768831G>A	ENST00000262738.3	-	25	7707	c.7708C>T	c.(7708-7710)Ccc>Tcc	p.P2570S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2570					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AACCGCATGGGCCCCGTGTCG	0.582																																					p.P2570S													.	CELSR1	242		0			c.C7708T												124.0	95.0	105.0					22																	46768831		2203	4300	6503	SO:0001583	missense	9620	exon25			GCATGGGCCCCGT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7708C>T	22.37:g.46768831G>A	ENSP00000262738:p.Pro2570Ser		Somatic	39	0	0		WXS	Illumina HiSeq		28	0.14	4	NM_014246	1	0.00	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	g	18.24	3.581367	0.65992	.	.	ENSG00000075275	ENST00000262738	T	0.36340	1.26	4.24	4.24	0.50183	GPCR, family 2-like (1);	0.076355	0.50627	U	0.000106	T	0.55097	0.1899	L	0.59436	1.845	0.80722	D	1	D;P	0.89917	1.0;0.932	D;P	0.79108	0.992;0.752	T	0.52888	-0.8515	10	0.31617	T	0.26	.	16.5871	0.84730	0.0:0.0:1.0:0.0	.	891;2570	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	S	2570	ENSP00000262738:P2570S	ENSP00000262738:P2570S	P	-	1	0	CELSR1	45147495	1.000000	0.71417	0.999000	0.59377	0.450000	0.32258	5.309000	0.65774	2.063000	0.61619	0.306000	0.20318	CCC			0.582	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318037.1		NM_014246	
POGLUT1	56983	broad.mit.edu	37	3	119204180	119204180	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr3:119204180C>T	ENST00000295588.4	+	6	668	c.584C>T	c.(583-585)gCa>gTa	p.A195V		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	195					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						CTTAGGTCAGCAGCACAGTGG	0.313																																					p.A195V													.	POGLUT1	32		0			c.C584T												85.0	94.0	91.0					3																	119204180		2203	4300	6503	SO:0001583	missense	56983	exon6			GGTCAGCAGCACA	BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"""KDELC family like 1"""	615618	"""chromosome 3 open reading frame 9"", ""KTEL (Lys-Tyr-Glu-Leu) containing 1"""	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.584C>T	3.37:g.119204180C>T	ENSP00000295588:p.Ala195Val		Somatic	289	0.0034602076	1		WXS	Illumina HiSeq	Phase_I	262	0.02	6	NM_152305	8	0.00	0	B2RD13|Q53GJ4|Q8N2T1	Missense_Mutation	SNP	ENST00000295588.4	37	CCDS2988.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373092	0.61624	.	.	ENSG00000163389	ENST00000295588	T	0.23754	1.89	5.32	5.32	0.75619	.	0.122334	0.53938	D	0.000042	T	0.27731	0.0682	L	0.43646	1.37	0.47511	D	0.99944	B	0.31859	0.343	B	0.37731	0.257	T	0.02966	-1.1088	10	0.35671	T	0.21	-16.1663	14.8705	0.70453	0.0:1.0:0.0:0.0	.	195	Q8NBL1	PGLT1_HUMAN	V	195	ENSP00000295588:A195V	ENSP00000295588:A195V	A	+	2	0	POGLUT1	120686870	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.013000	0.64023	2.634000	0.89283	0.655000	0.94253	GCA			0.313	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000355034.2		NM_152305	
NUP210P1	255330	broad.mit.edu	37	3	126385091	126385091	+	RNA	DEL	C	C	-	rs547540000|rs146507124	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr3:126385091delC	ENST00000357061.3	+	0	347					NR_034158.1				nucleoporin 210kDa pseudogene 1																		GGTGCTGCTGCTTGGAGCCGT	0.607													C|C|-|deletion	83	0.0165735	0.0166	0.0144	5008	,	,		18728	0.002		0.0427	False		,,,				2504	0.0061				.													.	.			0			.																																											0	.			CTGCTGCTTGGAG	BC042038		3q21.2	2011-08-16	2011-08-16	2011-08-16	ENSG00000198284	ENSG00000198284			27399	pseudogene	pseudogene			"""chromosome 3 open reading frame 46"""	C3orf46			Standard	NR_034158		Approved		uc003eje.1		OTTHUMG00000159577		3.37:g.126385091delC			Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	7	0.43	3	.	0		0		RNA	DEL	ENST00000357061.3	37																																																																																						0.607	NUP210P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000356320.1		NR_034158	
MSL2	55167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	135871188	135871188	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr3:135871188C>T	ENST00000309993.2	-	2	1267	c.535G>A	c.(535-537)Gaa>Aaa	p.E179K	MSL2_ENST00000434835.2_Missense_Mutation_p.E105K	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	179					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						AGGGTGCTTTCAGACATTGGA	0.398																																					p.E179K													.	.			0			c.G535A												73.0	68.0	70.0					3																	135871188		2203	4300	6503	SO:0001583	missense	55167	exon2			TGCTTTCAGACAT	AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"""RING-type (C3HC4) zinc fingers"""	25544	protein-coding gene	gene with protein product	"""male-specific lethal-2 homolog (Drosophila)"""	614802	"""ring finger protein 184"", ""male-specific lethal 2-like 1 (Drosophila)"""	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.535G>A	3.37:g.135871188C>T	ENSP00000311827:p.Glu179Lys		Somatic	126	0	0		WXS	Illumina HiSeq	.	132	0.21	28	NM_018133	14	0.36	5	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	37	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.881696	0.33255	.	.	ENSG00000174579	ENST00000309993;ENST00000434835;ENST00000481989;ENST00000491050	.	.	.	6.03	5.16	0.70880	.	0.244651	0.35013	N	0.003506	T	0.40522	0.1120	N	0.19112	0.55	0.46149	D	0.998898	B	0.20671	0.047	B	0.15484	0.013	T	0.24905	-1.0147	9	0.35671	T	0.21	-5.6657	10.1563	0.42825	0.0:0.793:0.1358:0.0712	.	179	Q9HCI7	MSL2_HUMAN	K	179;105;105;105	.	ENSP00000311827:E179K	E	-	1	0	MSL2	137353878	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.615000	0.54167	1.551000	0.49450	0.655000	0.94253	GAA			0.398	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000357347.1		NM_018133	
ZBBX	79740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	167034805	167034805	+	Silent	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr3:167034805G>A	ENST00000392766.2	-	14	1522	c.1182C>T	c.(1180-1182)gtC>gtT	p.V394V	ZBBX_ENST00000392764.1_Silent_p.V365V|ZBBX_ENST00000392767.2_Silent_p.V394V|ZBBX_ENST00000469220.1_5'UTR|ZBBX_ENST00000455345.2_Silent_p.V394V|ZBBX_ENST00000307529.5_Silent_p.V394V	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	394						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CATCCAGTTCGACTATCTTTA	0.343																																					p.V394V													.	.			0			c.C1182T												160.0	146.0	150.0					3																	167034805		1873	4095	5968	SO:0001819	synonymous_variant	79740	exon14			CAGTTCGACTATC	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1182C>T	3.37:g.167034805G>A			Somatic	96	0	0		WXS	Illumina HiSeq	.	142	0.15	22	NM_024687	0		0	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																					0.343	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000257657.3		NM_024687	
SPATA18	132671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	52943177	52943177	+	Missense_Mutation	SNP	G	G	A	rs193921037	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr4:52943177G>A	ENST00000295213.4	+	7	1365	c.991G>A	c.(991-993)Gtt>Att	p.V331I	SPATA18_ENST00000419395.2_Missense_Mutation_p.V299I	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	331					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			GGCTGAGACCGTTCAGCGGAT	0.622																																					p.V331I													SPATA18_ENST00000295213,NS,adenoma,0,2	SPATA18_ENST00000295213	0	2	0			c.G991A												30.0	23.0	25.0					4																	52943177		2203	4300	6503	SO:0001583	missense	132671	exon7			GAGACCGTTCAGC	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.991G>A	4.37:g.52943177G>A	ENSP00000295213:p.Val331Ile		Somatic	174	0	0		WXS	Illumina HiSeq	.	215	0.12	26	NM_145263	1	1.00	1	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.768603	0.69878	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.57107	0.42;1.55	3.99	3.99	0.46301	.	0.061082	0.64402	D	0.000004	T	0.66713	0.2817	L	0.59436	1.845	0.52099	D	0.999948	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.79108	0.986;0.992;0.991	T	0.66056	-0.6018	10	0.37606	T	0.19	-17.3931	14.3725	0.66849	0.0:0.0:1.0:0.0	.	299;331;331	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	I	331;299	ENSP00000295213:V331I;ENSP00000415309:V299I	ENSP00000295213:V331I	V	+	1	0	SPATA18	52637934	1.000000	0.71417	0.940000	0.37924	0.940000	0.58332	8.204000	0.89741	2.137000	0.66172	0.462000	0.41574	GTT			0.622	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000250597.2		NM_145263	
TMPRSS11E	28983	broad.mit.edu	37	4	69343244	69343244	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr4:69343244T>C	ENST00000305363.4	+	8	929	c.865T>C	c.(865-867)Tac>Cac	p.Y289H		NM_014058.3	NP_054777.2	Q9UL52	TM11E_HUMAN	transmembrane protease, serine 11E	289	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cognition (GO:0050890)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|lung(19)|pancreas(1)|skin(3)	24						CCCTGTTCCCTACACAAATGC	0.413																																					p.Y289H													.	TMPRSS11E	40		0			c.T865C												272.0	268.0	269.0					4																	69343244		2203	4300	6503	SO:0001583	missense	28983	exon8			GTTCCCTACACAA	AF064819	CCDS33993.1	4q13.2	2010-04-13			ENSG00000087128	ENSG00000087128		"""Serine peptidases / Transmembrane"""	24465	protein-coding gene	gene with protein product		610399	"""transmembrane protease, serine 11E2"""	TMPRSS11E2		15328353	Standard	NM_014058		Approved	DESC1	uc003hdz.4	Q9UL52	OTTHUMG00000160438	ENST00000305363.4:c.865T>C	4.37:g.69343244T>C	ENSP00000307519:p.Tyr289His		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	369	0.01	5	NM_014058	0		0	A6NL71|Q14DC8|Q6UW31	Missense_Mutation	SNP	ENST00000305363.4	37	CCDS33993.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.930622	0.73327	.	.	ENSG00000087128	ENST00000305363	T	0.60299	0.2	5.42	4.19	0.49359	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.150995	0.30949	N	0.008558	T	0.70971	0.3285	M	0.82056	2.57	0.24896	N	0.992131	D	0.57899	0.981	P	0.59761	0.863	T	0.64850	-0.6310	10	0.72032	D	0.01	.	10.0465	0.42190	0.1499:0.0:0.0:0.8501	.	289	Q9UL52	TM11E_HUMAN	H	289	ENSP00000307519:Y289H	ENSP00000307519:Y289H	Y	+	1	0	TMPRSS11E	69025839	0.997000	0.39634	0.999000	0.59377	0.970000	0.65996	2.940000	0.49003	2.052000	0.61016	0.477000	0.44152	TAC			0.413	TMPRSS11E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000360584.1		NM_014058	
NEIL3	55247	broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	178272589	178272589	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr4:178272589G>A	ENST00000264596.3	+	7	1043	c.925G>A	c.(925-927)Gtt>Att	p.V309I	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	309					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		GGTGGATCATGTTATGGACTC	0.403								Base excision repair (BER), DNA glycosylases																													p.V309I													.	NEIL3	89		0			c.G925A												157.0	146.0	150.0					4																	178272589		2203	4300	6503	SO:0001583	missense	55247	exon7			GATCATGTTATGG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.925G>A	4.37:g.178272589G>A	ENSP00000264596:p.Val309Ile		Somatic	72	0.0138888889	1		WXS	Illumina HiSeq	Phase_I	67	0.61	41	NM_018248	4	0.75	3	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	G	6.965	0.547937	0.13312	.	.	ENSG00000109674	ENST00000264596	T	0.03889	3.77	5.23	-1.02	0.10135	.	0.829839	0.10785	N	0.634440	T	0.01940	0.0061	N	0.08118	0	0.09310	N	1	B	0.18610	0.029	B	0.12837	0.008	T	0.48603	-0.9021	10	0.15066	T	0.55	-0.4081	2.1422	0.03777	0.1167:0.142:0.3297:0.4116	.	309	Q8TAT5	NEIL3_HUMAN	I	309	ENSP00000264596:V309I	ENSP00000264596:V309I	V	+	1	0	NEIL3	178509583	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.072000	0.03434	0.027000	0.15297	-0.165000	0.13383	GTT			0.403	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000361914.1		NM_018248	
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	187557879	187557879	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr4:187557879C>T	ENST00000441802.2	-	5	4041	c.3832G>A	c.(3832-3834)Gac>Aac	p.D1278N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1278	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TCATCCTTGTCGGTGGCTATG	0.498										HNSCC(5;0.00058)																											p.D1278N	Colon(197;1040 2055 4143 4984 49344)												.	.			0			c.G3832A												215.0	217.0	216.0					4																	187557879		1888	4114	6002	SO:0001583	missense	2195	exon5			CCTTGTCGGTGGC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.3832G>A	4.37:g.187557879C>T	ENSP00000406229:p.Asp1278Asn		Somatic	115	0	0		WXS	Illumina HiSeq	.	164	0.19	31	NM_005245	0		0		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.121381	0.77436	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.74526	-0.85	4.99	4.99	0.66335	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92779	0.7704	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95905	0.8918	10	0.87932	D	0	.	18.4667	0.90758	0.0:1.0:0.0:0.0	.	1278	Q14517	FAT1_HUMAN	N	1278	ENSP00000406229:D1278N	ENSP00000260147:D1278N	D	-	1	0	FAT1	187794873	1.000000	0.71417	0.956000	0.39512	0.090000	0.18270	7.651000	0.83577	2.599000	0.87857	0.561000	0.74099	GAC			0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000360209.3		NM_005245	
PRLR	5618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	35065642	35065642	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr5:35065642G>A	ENST00000382002.5	-	10	1844	c.1418C>T	c.(1417-1419)gCa>gTa	p.A473V	PRLR_ENST00000542609.1_Intron|PRLR_ENST00000231423.3_Intron|PRLR_ENST00000342362.5_Missense_Mutation_p.A372V|PRLR_ENST00000310101.5_Intron|PRLR_ENST00000397391.3_Intron|PRLR_ENST00000348262.3_Intron|PRLR_ENST00000513753.1_Intron|PRLR_ENST00000509934.1_5'Flank|PRLR_ENST00000511486.1_Missense_Mutation_p.A372V	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	473					activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	CTGCTGGGTTGCCTTTCCCTC	0.537																																					p.A473V													PRLR,NS,carcinoma,-1,1	PRLR	-1	1	0			c.C1418T												87.0	96.0	93.0					5																	35065642		2203	4300	6503	SO:0001583	missense	5618	exon10			TGGGTTGCCTTTC		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.1418C>T	5.37:g.35065642G>A	ENSP00000371432:p.Ala473Val		Somatic	157	0	0		WXS	Illumina HiSeq	.	136	0.35	48	NM_000949	2	0.00	0	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	G	0.106	-1.144787	0.01714	.	.	ENSG00000113494	ENST00000342362;ENST00000382002;ENST00000511486	D;T;D	0.87809	-2.3;-1.38;-2.3	5.8	-0.817	0.10836	.	0.829110	0.11512	N	0.556610	T	0.77246	0.4102	L	0.55834	1.745	0.09310	N	1	B;B	0.22003	0.021;0.063	B;B	0.18871	0.013;0.023	T	0.57359	-0.7825	10	0.13470	T	0.59	-0.6824	1.0468	0.01571	0.2163:0.1851:0.3806:0.218	.	473;372	P16471;P16471-2	PRLR_HUMAN;.	V	372;473;372	ENSP00000339213:A372V;ENSP00000371432:A473V;ENSP00000422556:A372V	ENSP00000339213:A372V	A	-	2	0	PRLR	35101399	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.272000	0.08560	-0.145000	0.11294	-0.140000	0.14226	GCA			0.537	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000207575.2			
PAIP1	10605	hgsc.bcm.edu	37	5	43539098	43539098	+	Silent	SNP	T	T	C			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr5:43539098T>C	ENST00000306846.3	-	5	1006	c.774A>G	c.(772-774)aaA>aaG	p.K258K	PAIP1_ENST00000436644.2_Silent_p.K179K|PAIP1_ENST00000514514.1_Silent_p.K179K|PAIP1_ENST00000338972.4_Silent_p.K146K	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	258	MIF4G.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)			endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					CTTCATCCCCTTTTGCAGCTT	0.323																																					p.K258K													.	.			0			c.A774G												150.0	143.0	145.0					5																	43539098		2203	4300	6503	SO:0001819	synonymous_variant	10605	exon5			ATCCCCTTTTGCA	AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.774A>G	5.37:g.43539098T>C			Somatic	54	0	0		WXS	Illumina HiSeq	.	61	0.07	4	NM_006451	45	0.00	0	A6NKV8|O60455|Q96B61|Q9BS63	Silent	SNP	ENST00000306846.3	37	CCDS3947.1																																																																																					0.323	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000214024.1		NM_006451	
CMAHP	8418	broad.mit.edu	37	6	25091943	25091945	+	RNA	DEL	ATA	ATA	-	rs10570782|rs199656242	byFrequency	TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	ATA	ATA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr6:25091943_25091945delATA	ENST00000377989.4	-	0	1962							Q9Y471	CMAH_HUMAN	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene						CMP-N-acetylneuraminate metabolic process (GO:0046381)	cytoplasm (GO:0005737)	2 iron, 2 sulfur cluster binding (GO:0051537)|oxidoreductase activity (GO:0016491)			NS(1)	1						tgtattaattataattatattaa	0.187														942	0.188099	0.1346	0.2392	5008	,	,		9661	0.2302		0.1928	False		,,,				2504	0.1759				.													.	CMAHP	6		0			.																																											0	.			TTAATTATAATTA			6p23-p22	2011-04-28	2011-04-28	2011-04-28	ENSG00000168405	ENSG00000168405			2098	pseudogene	pseudogene		603209	"""cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMP-N-acetylneuraminate monooxygenase)(pseudogene)"""	CMAH		7608218, 9624188	Standard	NR_002174		Approved		uc003ner.4	Q9Y471	OTTHUMG00000016099		6.37:g.25091943_25091945delATA			Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	9	0.22	2	.	0		0	O95250|Q5TD41|Q5TD42|Q5TD43|Q5TD44|Q68DC3|Q9UEE7	RNA	DEL	ENST00000377989.4	37																																																																																						0.187	CMAHP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000043292.2		NR_002174	
MYO6	4646	broad.mit.edu	37	6	76591494	76591494	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr6:76591494G>T	ENST00000369977.3	+	23	2514	c.2375G>T	c.(2374-2376)cGc>cTc	p.R792L	MYO6_ENST00000462633.1_3'UTR|MYO6_ENST00000369985.4_Missense_Mutation_p.R792L|MYO6_ENST00000369975.1_Missense_Mutation_p.R792L|MYO6_ENST00000369981.3_Missense_Mutation_p.R792L	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	792	Required for binding calmodulin. {ECO:0000250}.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		ACATGCAGTCGCTGGAAGAAA	0.418																																					p.R792L													MYO6,NS,carcinoma,+1,1	MYO6	124	1	0			c.G2375T												146.0	140.0	142.0					6																	76591494		2203	4300	6503	SO:0001583	missense	4646	exon23			GCAGTCGCTGGAA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2375G>T	6.37:g.76591494G>T	ENSP00000358994:p.Arg792Leu		Somatic	100	0.01	1		WXS	Illumina HiSeq	Phase_I	91	0.03	3	NM_004999	5	0.00	0	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172508	0.94807	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.85750	0.5769	M	0.88377	2.95	0.80722	D	1	P;D	0.89917	0.757;1.0	P;D	0.91635	0.508;0.999	D	0.87696	0.2557	10	0.72032	D	0.01	.	19.4895	0.95044	0.0:0.0:1.0:0.0	.	792;792	Q9UM54-2;Q9UM54-1	.;.	L	792	ENSP00000358998:R792L;ENSP00000359002:R792L;ENSP00000358994:R792L;ENSP00000358992:R792L	ENSP00000358992:R792L	R	+	2	0	MYO6	76648214	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.447000	0.97595	2.596000	0.87737	0.655000	0.94253	CGC			0.418	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041279.2		NM_004999	
MOXD1	26002	broad.mit.edu;bcgsc.ca	37	6	132643950	132643950	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr6:132643950G>T	ENST00000367963.3	-	8	1291	c.1173C>A	c.(1171-1173)caC>caA	p.H391Q	MOXD1_ENST00000336749.3_Missense_Mutation_p.H323Q|MOXD1_ENST00000489128.1_5'UTR	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	391						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TGCCAGCCAGGTGAGCATGGA	0.463																																					p.H391Q													.	MOXD1	136		0			c.C1173A												89.0	81.0	84.0					6																	132643950		2203	4300	6503	SO:0001583	missense	26002	exon8			AGCCAGGTGAGCA	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1173C>A	6.37:g.132643950G>T	ENSP00000356940:p.His391Gln		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	0.05	7	NM_015529	7	0.00	0	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	G	21.6	4.168605	0.78339	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	D;D	0.91843	-2.92;-2.92	5.78	4.73	0.59995	PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96562	0.8878	M	0.91090	3.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.96894	0.9655	10	0.87932	D	0	-25.4137	15.7174	0.77677	0.0762:0.0:0.9238:0.0	.	391;323	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	Q	391;323	ENSP00000356940:H391Q;ENSP00000336998:H323Q	ENSP00000336998:H323Q	H	-	3	2	MOXD1	132685643	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.508000	0.35769	2.733000	0.93635	0.655000	0.94253	CAC			0.463	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000125837.1		NM_015529	
RAPGEF5	9771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	22348122	22348122	+	Silent	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr7:22348122G>A	ENST00000405243.1	-	5	599	c.516C>T	c.(514-516)gaC>gaT	p.D172D	RAPGEF5_ENST00000344041.6_Silent_p.D19D			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	0	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						ATAGATGCTGGTCCACTGTTT	0.299																																					p.D19D													.	.			0			c.C57T												45.0	40.0	41.0					7																	22348122		1821	4057	5878	SO:0001819	synonymous_variant	9771	exon5			ATGCTGGTCCACT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000405243.1:c.516C>T	7.37:g.22348122G>A			Somatic	55	0	0		WXS	Illumina HiSeq	.	90	0.10	9	NM_012294	0		0	A4D140|Q8IXU5	Silent	SNP	ENST00000405243.1	37																																																																																						0.299	RAPGEF5-002	PUTATIVE	basic	protein_coding	protein_coding		OTTHUMT00000326591.1		NM_012294	
GTF2IRD2P1	401375	broad.mit.edu	37	7	72663998	72663998	+	RNA	SNP	T	T	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr7:72663998T>G	ENST00000425256.1	-	0	902									GTF2I repeat domain containing 2 pseudogene 1																		ATAGCCGGGGTCCTTGAATAC	0.488																																					.													.	.			0			.																																											0	.			CCGGGGTCCTTGA	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72663998T>G			Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	134	0.03	4	.	0		0		RNA	SNP	ENST00000425256.1	37																																																																																						0.488	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000345921.1		NR_002164	
GTF2IRD2P1	401375	broad.mit.edu	37	7	72669802	72669802	+	RNA	DEL	A	A	-			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr7:72669802delA	ENST00000425256.1	-	0	567									GTF2I repeat domain containing 2 pseudogene 1																		TGGAATCTTGAAAAAAAAATG	0.393																																					.													.	.			0			.																																											0	.			ATCTTGAAAAAAA	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72669802delA			Somatic	451	0.0110864745	5		WXS	Illumina HiSeq	Phase_I	550	0.02	10	.	0		0		RNA	DEL	ENST00000425256.1	37																																																																																						0.393	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000345921.1		NR_002164	
LOC101927126	101927126	broad.mit.edu	37	7	75730186	75730186	+	RNA	DEL	T	T	-			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr7:75730186delT	ENST00000434037.1	-	0	424																											CATTTTATTGTTTTAATTCCA	0.388																																					.													.	.			0			.																																											0	.			TTATTGTTTTAAT																													7.37:g.75730186delT			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000434037.1	37																																																																																						0.388	AC005077.12-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000344843.1			
FLNC	2318	broad.mit.edu	37	7	128478446	128478446	+	Silent	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr7:128478446G>T	ENST00000325888.8	+	7	1434	c.1173G>T	c.(1171-1173)gtG>gtT	p.V391V	FLNC_ENST00000346177.6_Silent_p.V391V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	391					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TGGGCAATGTGGCCAACAAAC	0.617																																					p.V391V													.	FLNC	339		0			c.G1173T												110.0	117.0	115.0					7																	128478446		2077	4197	6274	SO:0001819	synonymous_variant	2318	exon7			CAATGTGGCCAAC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.1173G>T	7.37:g.128478446G>T			Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	106	0.04	4	NM_001127487	11	0.00	0	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																					0.617	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000059948.3			
CALB1	793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	91078131	91078131	+	Silent	SNP	G	G	A			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr8:91078131G>A	ENST00000265431.3	-	6	626	c.445C>T	c.(445-447)Cta>Tta	p.L149L	CALB1_ENST00000518457.1_Silent_p.L92L	NM_004929.2	NP_004920.1	P05937	CALB1_HUMAN	calbindin 1, 28kDa	149	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to organic substance (GO:0071310)|cytosolic calcium ion homeostasis (GO:0051480)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|metanephric collecting duct development (GO:0072205)|metanephric connecting tubule development (GO:0072286)|metanephric distal convoluted tubule development (GO:0072221)|metanephric part of ureteric bud development (GO:0035502)|regulation of synaptic plasticity (GO:0048167)|retina layer formation (GO:0010842)|short-term memory (GO:0007614)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|vitamin D binding (GO:0005499)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(8)|pancreas(1)	11			BRCA - Breast invasive adenocarcinoma(11;0.00953)			CTTACCATTAGGTCTGTATAC	0.353																																					p.L149L	Melanoma(46;573 1182 27367 39727 48386)												.	.			0			c.C445T												121.0	108.0	113.0					8																	91078131		2203	4300	6503	SO:0001819	synonymous_variant	793	exon6			CCATTAGGTCTGT		CCDS6251.1	8q21.3	2013-01-10	2002-08-29		ENSG00000104327	ENSG00000104327		"""EF-hand domain containing"""	1434	protein-coding gene	gene with protein product		114050		CALB			Standard	NM_004929		Approved		uc003yel.1	P05937	OTTHUMG00000134314	ENST00000265431.3:c.445C>T	8.37:g.91078131G>A			Somatic	114	0	0		WXS	Illumina HiSeq	.	120	0.13	16	NM_004929	74	0.24	18	B2R696|B7Z9J4	Silent	SNP	ENST00000265431.3	37	CCDS6251.1																																																																																					0.353	CALB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000259338.2		NM_004929	
GRHL2	79977	broad.mit.edu	37	8	102585952	102585952	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chr8:102585952A>G	ENST00000251808.3	+	6	1129	c.791A>G	c.(790-792)gAg>gGg	p.E264G	GRHL2_ENST00000395927.1_Missense_Mutation_p.E248G	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	264					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			AAGCAGGGGGAGGGCCCCATG	0.517																																					p.E264G													.	GRHL2	68		0			c.A791G												75.0	63.0	67.0					8																	102585952		2203	4300	6503	SO:0001583	missense	79977	exon6			AGGGGGAGGGCCC	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.791A>G	8.37:g.102585952A>G	ENSP00000251808:p.Glu264Gly		Somatic	124	0.0080645161	1		WXS	Illumina HiSeq	Phase_I	178	0.02	4	NM_024915	2	0.00	0	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	37	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.921271	0.92249	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.28895	1.59;1.59	5.8	5.8	0.92144	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.62295	0.2416	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.991	T	0.69480	-0.5134	10	0.87932	D	0	-38.965	16.1475	0.81580	1.0:0.0:0.0:0.0	.	264;264	B4DL28;Q6ISB3	.;GRHL2_HUMAN	G	264;248;264	ENSP00000251808:E264G;ENSP00000379260:E248G	ENSP00000251808:E264G	E	+	2	0	GRHL2	102655128	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.307000	0.96226	2.213000	0.71641	0.528000	0.53228	GAG			0.517	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000313882.1		NM_024915	
MT-ND4	4538	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	M	12077	12077	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chrM:12077C>T	ENST00000361381.2	+	1	1318	c.1318C>T	c.(1318-1320)Cac>Tac	p.H440Y	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	440					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TCATGTTCATACACCTATCCC	0.428																																					p.H440Y													.	.			0			c.C1318T																																									SO:0001583	missense	0	exon1			TTCATACACCTAT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1318C>T	M.37:g.12077C>T	ENSP00000354961:p.His440Tyr		Somatic	20	0	0		WXS	Illumina HiSeq	.	33	0.76	25	ENST00000361381	0		0	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																						0.428	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024035	
MT-CYB	4519	bcgsc.ca	37	M	15639	15639	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chrM:15639T>C	ENST00000361789.2	+	1	893	c.893T>C	c.(892-894)aTc>aCc	p.I298T	MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	298					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						ATTACTATCCATCCTCATCCT	0.458											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.I298T													.	.			0			c.T893C																																									SO:0001583	missense	0	exon1			TATCCATCCTCAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.893T>C	M.37:g.15639T>C	ENSP00000354554:p.Ile298Thr		Somatic	18	0.0555555556	1	585	WXS	Illumina HiSeq	Phase_1	38	0.92	35	ENST00000361789	0		0	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																						0.458	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024038	
RBM3	5935	ucsc.edu	37	X	48434994	48434994	+	Splice_Site	SNP	T	T	G			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chrX:48434994T>G	ENST00000376759.3	+	5	476		c.e5+2		RBM3_ENST00000376755.1_Splice_Site|RBM3_ENST00000466764.1_Splice_Site|RBM3_ENST00000430348.2_Splice_Site|AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000354480.2_Splice_Site	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3						positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)	p.?(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TAATGGCAGGTGGGTAGCCAA	0.517																																					.													.	RBM3	20		1	Unknown(1)	ovary(1)	c.413+2T>G												59.0	56.0	57.0					X																	48434994		2193	4272	6465	SO:0001630	splice_region_variant	5935	exon5			GGCAGGTGGGTAG	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"""RNA binding motif (RRM) containing"""	9900	protein-coding gene	gene with protein product		300027	"""RNA binding motif protein 3"""			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.413+2T>G	X.37:g.48434994T>G			Somatic	39	0.1794871795	7		WXS	Illumina HiSeq		54	0.28	15	NM_006743	2	0.00	0		Splice_Site	SNP	ENST00000376759.3	37	CCDS14301.1	.	.	.	.	.	.	.	.	.	.	t	11.97	1.798592	0.31777	.	.	ENSG00000102317	ENST00000376759;ENST00000430348;ENST00000376755;ENST00000354480	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3004	0.43648	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM3	48319938	1.000000	0.71417	0.999000	0.59377	0.387000	0.30353	2.025000	0.41059	1.792000	0.52537	0.481000	0.45027	.			0.517	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000060755.1		NM_006743	Intron
TERF1P4	648283	bcgsc.ca	37	X	83004722	83004722	+	IGR	SNP	G	G	T			TCGA-2G-AAKD-01A-31D-A42Y-10	TCGA-2G-AAKD-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26d84898-bffe-4bf2-98b3-e2745b224de3	32a4f026-dca8-4f8c-81e8-2d7e8ea2d166	g.chrX:83004722G>T								RP3-326L13.3 (237587 upstream) : CYLC1 (111431 downstream)																							TTTTCAAATTGTGCATCAAGG	0.363																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	648283	.			CAAATTGTGCATC																													X.37:g.83004722G>T			Somatic	58	0	0		WXS	Illumina HiSeq	Phase_1	86	0.42	36	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.363										
