#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ADAMTS13	11093	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	136291396	136291396	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr9:136291396delG	ENST00000371929.3	+	6	1061	c.617delG	c.(616-618)tggfs	p.W206fs	ADAMTS13_ENST00000536611.1_5'Flank|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000356589.2_Frame_Shift_Del_p.W206fs|ADAMTS13_ENST00000371911.3_Frame_Shift_Del_p.W206fs|ADAMTS13_ENST00000371916.1_Frame_Shift_Del_p.W206fs|ADAMTS13_ENST00000355699.2_Frame_Shift_Del_p.W206fs	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	206	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCCCCAACCTGGAGCTGCCTC	0.607																																																	0													74.0	64.0	67.0					9																	136291396		2203	4300	6503	SO:0001589	frameshift_variant	11093			AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.617delG	9.37:g.136291396delG	ENSP00000360997:p.Trp206fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Frame_Shift_Del	DEL	ENST00000371929.3	37	CCDS6970.1																																																																																				0.607	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1		NM_139025	
ART1	417	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	3681532	3681532	+	Silent	SNP	C	C	T	rs139469651	byFrequency	TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr11:3681532C>T	ENST00000250693.1	+	3	884	c.783C>T	c.(781-783)ccC>ccT	p.P261P		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	261					innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		CCCAGGGCCCCGCCCGCATCT	0.602													C|||	3	0.000599042	0.0023	0.0	5008	,	,		17767	0.0		0.0	False		,,,				2504	0.0																0								C		1,4401	2.1+/-5.4	0,1,2200	43.0	47.0	46.0		783	-10.0	0.0	11	dbSNP_134	46	0,8594		0,0,4297	no	coding-synonymous	ART1	NM_004314.2		0,1,6497	TT,TC,CC		0.0,0.0227,0.0077		261/328	3681532	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	417			S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"""CD molecules"""	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.783C>T	11.37:g.3681532C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6NTD2|Q96KT9	Silent	SNP	ENST00000250693.1	37	CCDS7744.1																																																																																				0.602	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1		NM_004314	
ASTL	431705	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	96789912	96789912	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr2:96789912G>T	ENST00000342380.2	-	9	972	c.973C>A	c.(973-975)Ccc>Acc	p.P325T		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						GAACCACTGGGGTCGGGGCTC	0.672																																																	0													23.0	28.0	26.0					2																	96789912		2199	4290	6489	SO:0001583	missense	431705			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.973C>A	2.37:g.96789912G>T	ENSP00000343674:p.Pro325Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000342380.2	37	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.457817	0.26161	.	.	ENSG00000188886	ENST00000342380	T	0.71222	-0.55	4.41	2.55	0.30701	.	0.533769	0.14188	N	0.335558	T	0.54711	0.1875	L	0.29908	0.895	0.09310	N	1	B	0.20052	0.041	B	0.14578	0.011	T	0.48581	-0.9023	10	0.62326	D	0.03	0.1193	5.5058	0.16854	0.1059:0.0:0.6974:0.1967	.	325	Q6HA08	ASTL_HUMAN	T	325	ENSP00000343674:P325T	ENSP00000343674:P325T	P	-	1	0	ASTL	96153639	0.000000	0.05858	0.002000	0.10522	0.059000	0.15707	-0.309000	0.08145	0.407000	0.25591	0.306000	0.20318	CCC		0.672	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			
C9orf16	79095	hgsc.bcm.edu	37	9	130925841	130925841	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr9:130925841C>T	ENST00000372994.1	+	2	347	c.199C>T	c.(199-201)Cgc>Tgc	p.R67C	C9orf16_ENST00000492588.1_3'UTR	NM_024112.3	NP_077017.1	Q9BUW7	CI016_HUMAN	chromosome 9 open reading frame 16	67										ovary(1)	1		Myeloproliferative disorder(762;0.0511)		GBM - Glioblastoma multiforme(294;0.0294)		CCGGCAGACACGCCTGGAGTT	0.657																																																	0													24.0	24.0	24.0					9																	130925841		2203	4300	6503	SO:0001583	missense	79095			AK022885	CCDS6893.1	9q34.1	2012-03-06			ENSG00000171159	ENSG00000171159			17823	protein-coding gene	gene with protein product						10369878	Standard	NM_024112		Approved	EST00098, FLJ12823, MGC4639	uc004btp.1	Q9BUW7	OTTHUMG00000020731	ENST00000372994.1:c.199C>T	9.37:g.130925841C>T	ENSP00000362085:p.Arg67Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5SYV8|Q9Y3F7	Missense_Mutation	SNP	ENST00000372994.1	37	CCDS6893.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534138	0.85812	.	.	ENSG00000171159	ENST00000372994	.	.	.	5.34	3.3	0.37823	.	0.058514	0.64402	D	0.000003	T	0.49321	0.1550	.	.	.	0.58432	D	0.999994	B	0.26635	0.155	B	0.23852	0.049	T	0.54357	-0.8306	8	0.87932	D	0	-13.4923	11.6081	0.51043	0.1326:0.7953:0.0:0.072	.	67	Q9BUW7	CI016_HUMAN	C	67	.	ENSP00000362085:R67C	R	+	1	0	C9orf16	129965662	0.975000	0.34042	0.988000	0.46212	0.997000	0.91878	2.470000	0.45119	1.270000	0.44297	0.555000	0.69702	CGC		0.657	C9orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054351.1		NM_024112	
CILP	8483	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	65499358	65499358	+	Silent	SNP	G	G	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr15:65499358G>T	ENST00000261883.4	-	4	352	c.186C>A	c.(184-186)atC>atA	p.I62I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	62					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						CTGGGTAGTCGATGTTGAACC	0.597																																																	0													53.0	43.0	46.0					15																	65499358		2201	4299	6500	SO:0001819	synonymous_variant	8483			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.186C>A	15.37:g.65499358G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																				0.597	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1		NM_003613	
FAM124A	220108	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	51826047	51826047	+	Missense_Mutation	SNP	A	A	T	rs538055450		TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr13:51826047A>T	ENST00000322475.8	+	3	679	c.544A>T	c.(544-546)Aac>Tac	p.N182Y	FAM124A_ENST00000280057.6_Missense_Mutation_p.N218Y	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	182								p.N218Y(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TCGCTACGACAACTATGCTGA	0.577																																																	1	Substitution - Missense(1)	kidney(1)											47.0	45.0	46.0					13																	51826047		2203	4300	6503	SO:0001583	missense	220108			AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.544A>T	13.37:g.51826047A>T	ENSP00000324625:p.Asn182Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852676	0.51270	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.54866	0.55;0.55	5.79	5.79	0.91817	.	0.137789	0.64402	D	0.000006	T	0.71239	0.3316	M	0.75085	2.285	0.44067	D	0.996818	D;D;D	0.67145	0.996;0.993;0.978	D;P;P	0.65874	0.939;0.858;0.804	T	0.75164	-0.3414	10	0.87932	D	0	-24.0251	15.3036	0.73976	1.0:0.0:0.0:0.0	.	182;218;182	Q86V42;Q86V42-2;Q86V42-3	F124A_HUMAN;.;.	Y	182;218	ENSP00000324625:N182Y;ENSP00000280057:N218Y	ENSP00000280057:N218Y	N	+	1	0	FAM124A	50724048	1.000000	0.71417	0.866000	0.34008	0.018000	0.09664	8.962000	0.93254	2.208000	0.71279	0.533000	0.62120	AAC		0.577	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3		NM_145019	
HIST2H3D	653604	broad.mit.edu;hgsc.bcm.edu	37	1	149785229	149785229	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr1:149785229C>T	ENST00000331491.1	-	1	7	c.8G>A	c.(7-9)cGt>cAt	p.R3H	HIST2H2BF_ENST00000469483.1_5'Flank|HIST2H2BF_ENST00000369167.1_5'Flank|HIST2H2BF_ENST00000427880.2_5'Flank|HIST2H2BF_ENST00000545683.1_5'Flank|RP11-196G18.21_ENST00000420462.1_RNA	NM_001123375.2	NP_001116847.1	Q71DI3	H32_HUMAN	histone cluster 2, H3d	3					blood coagulation (GO:0007596)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			biliary_tract(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(3)	7						CTGCTTAGTACGGGCCATGCT	0.572																																																	0													31.0	32.0	32.0					1																	149785229		1565	3566	5131	SO:0001583	missense	653604			AL591493	CCDS41388.1	1q21.2	2012-03-08	2006-10-11		ENSG00000183598	ENSG00000183598		"""Histones / Replication-dependent"""	25311	protein-coding gene	gene with protein product			"""histone 2, H3d"""				Standard	NM_001123375		Approved		uc010pbl.2	Q71DI3	OTTHUMG00000012092	ENST00000331491.1:c.8G>A	1.37:g.149785229C>T	ENSP00000333277:p.Arg3His	Somatic		WXS	Illumina HiSeq	Phase_I	A2BDF6|A6NFS4|Q6B053	Missense_Mutation	SNP	ENST00000331491.1	37	CCDS41388.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046860	0.75846	.	.	ENSG00000183598	ENST00000331491	T	0.46819	0.86	4.13	4.13	0.48395	.	0.000000	0.51477	U	0.000086	T	0.54983	0.1892	.	.	.	0.49051	D	0.999747	.	.	.	.	.	.	T	0.60525	-0.7246	7	0.62326	D	0.03	.	15.4963	0.75653	0.0:1.0:0.0:0.0	.	.	.	.	H	3	ENSP00000333277:R3H	ENSP00000333277:R3H	R	-	2	0	HIST2H3D	148051853	0.037000	0.19845	0.176000	0.23000	0.169000	0.22640	2.716000	0.47219	2.302000	0.77476	0.436000	0.28706	CGT		0.572	HIST2H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033452.1		NM_001123375	
KCNF1	3754	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	11053935	11053935	+	Silent	SNP	G	G	A			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr2:11053935G>A	ENST00000295082.1	+	1	1873	c.1383G>A	c.(1381-1383)gcG>gcA	p.A461A		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	461					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		GGAAGGAGGCGCCGAGCTGCA	0.662																																																	0													16.0	22.0	20.0					2																	11053935		2200	4290	6490	SO:0001819	synonymous_variant	3754			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1383G>A	2.37:g.11053935G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O43527|Q585L3	Silent	SNP	ENST00000295082.1	37	CCDS1676.1																																																																																				0.662	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1		NM_002236	
MAGI1	9223	broad.mit.edu;hgsc.bcm.edu	37	3	65425588	65425588	+	Silent	SNP	C	C	T	rs374381483|rs139785185		TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr3:65425588C>T	ENST00000497477.2	-	9	1235	c.1236G>A	c.(1234-1236)caG>caA	p.Q412Q	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000402939.2_Silent_p.Q412Q|MAGI1_ENST00000330909.8_Silent_p.Q412Q|MAGI1_ENST00000483466.1_Silent_p.Q412Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	412	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		gctgctgctgctgttgctgct	0.537											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0								C	,,	0,4386		0,0,2193	59.0	59.0	59.0		1236,1236,1236	-0.3	0.1	3	dbSNP_134	59	6,8526		0,6,4260	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGI1	NM_001033057.1,NM_004742.2,NM_015520.1	,,	0,6,6453	TT,TC,CC		0.0703,0.0,0.0464	,,	412/1463,412/1257,412/1288	65425588	6,12912	2193	4266	6459	SO:0001819	synonymous_variant	9223			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1236G>A	3.37:g.65425588C>T		Somatic	1084	WXS	Illumina HiSeq	Phase_I	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	1.644	-0.515844	0.04200	0.0	7.03E-4	ENSG00000151276	ENST00000460329	.	.	.	2.7	-0.305	0.12784	.	.	.	.	.	T	0.50222	0.1603	.	.	.	0.47511	D	0.999444	.	.	.	.	.	.	T	0.34675	-0.9819	4	.	.	.	.	4.9509	0.14013	0.0:0.4601:0.2291:0.3109	.	.	.	.	N	293	.	.	S	-	2	0	MAGI1	65400628	0.923000	0.31300	0.067000	0.19924	0.012000	0.07955	0.342000	0.19926	-0.240000	0.09696	-0.808000	0.03180	AGC		0.537	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2		NM_004742	
MEOX1	4222	broad.mit.edu;hgsc.bcm.edu	37	17	41738797	41738797	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr17:41738797G>T	ENST00000318579.4	-	1	525	c.106C>A	c.(106-108)Ccc>Acc	p.P36T	MEOX1_ENST00000329168.3_Missense_Mutation_p.P36T|MEOX1_ENST00000393661.2_Intron|MEOX1_ENST00000549132.1_Nonsense_Mutation_p.Y6*	NM_001040002.1|NM_004527.3	NP_001035091.1|NP_004518.1	P50221	MEOX1_HUMAN	mesenchyme homeobox 1	36					multicellular organismal development (GO:0007275)|somite specification (GO:0001757)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P36T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		GGGTAGTGGGGTAGCCCTGAG	0.672																																																	1	Substitution - Missense(1)	kidney(1)											21.0	27.0	25.0					17																	41738797		2191	4291	6482	SO:0001583	missense	4222				CCDS11466.1, CCDS11467.1, CCDS42343.1	17q21.31	2014-07-15	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	7013	protein-coding gene	gene with protein product		600147	"""mesenchyme homeo box 1"""			7987315	Standard	NM_013999		Approved	MOX1	uc002idz.3	P50221	OTTHUMG00000170513	ENST00000318579.4:c.106C>A	17.37:g.41738797G>T	ENSP00000321684:p.Pro36Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K524|A8MWF9|Q15069	Missense_Mutation	SNP	ENST00000318579.4	37	CCDS11466.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.397277|5.397277	0.96009|0.96009	.|.	.|.	ENSG00000005102|ENSG00000005102	ENST00000318579;ENST00000329168|ENST00000549132	D;T|.	0.90620|.	-2.7;0.95|.	4.68|4.68	3.68|3.68	0.42216|0.42216	.|.	0.578526|.	0.18278|.	N|.	0.146111|.	T|.	0.32466|.	0.0830|.	L|L	0.44542|0.44542	1.39|1.39	0.22796|0.22796	N|N	0.998727|0.998727	B;B|.	0.34181|.	0.386;0.44|.	B;B|.	0.31101|.	0.124;0.118|.	T|.	0.22034|.	-1.0228|.	10|.	0.33141|0.13853	T|T	0.24|0.58	-18.6574|-18.6574	5.1692|5.1692	0.15101|0.15101	0.0823:0.1417:0.6301:0.1459|0.0823:0.1417:0.6301:0.1459	.|.	36;36|.	Q15069;P50221|.	.;MEOX1_HUMAN|.	T|X	36|6	ENSP00000321684:P36T;ENSP00000328678:P36T|.	ENSP00000321684:P36T|ENSP00000449049:Y6X	P|Y	-|-	1|3	0|2	MEOX1|MEOX1	39094323|39094323	0.924000|0.924000	0.31332|0.31332	0.961000|0.961000	0.40146|0.40146	0.992000|0.992000	0.81027|0.81027	1.284000|1.284000	0.33249|0.33249	1.155000|1.155000	0.42497|0.42497	0.563000|0.563000	0.77884|0.77884	CCC|TAC		0.672	MEOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409452.1			
PRSS16	10279	hgsc.bcm.edu	37	6	27218496	27218497	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr6:27218496_27218497insC	ENST00000230582.3	+	5	517_518	c.502_503insC	c.(502-504)tccfs	p.S168fs	PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	168					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CCTGGCACTTTCCCGCCTCTTT	0.629																																					NSCLC(178;1118 2105 17078 23587 44429)												0																																										SO:0001589	frameshift_variant	10279			AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.505dupC	6.37:g.27218499_27218499dupC	ENSP00000230582:p.Ser168fs	Somatic		WXS	Illumina HiSeq	Phase_I	O75416	Frame_Shift_Ins	INS	ENST00000230582.3	37	CCDS4623.1																																																																																				0.629	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			
SETD1A	9739	hgsc.bcm.edu	37	16	30975991	30975992	+	Frame_Shift_Ins	INS	-	-	C	rs76624905|rs146035438		TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr16:30975991_30975992insC	ENST00000262519.8	+	7	1614_1615	c.928_929insC	c.(928-930)tccfs	p.S310fs		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	310	Ser-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.S310F(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						AGATGCCTTTTCCCGCCGCCAC	0.599																																																	1	Substitution - Missense(1)	skin(1)																																								SO:0001589	frameshift_variant	9739			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.931dupC	16.37:g.30975994_30975994dupC	ENSP00000262519:p.Ser310fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NP62|Q6PIF3|Q8TAJ6	Frame_Shift_Ins	INS	ENST00000262519.8	37	CCDS32435.1																																																																																				0.599	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2		NM_014712	
SUSD2	56241	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	24580140	24580140	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr22:24580140A>C	ENST00000358321.3	+	4	737	c.476A>C	c.(475-477)gAg>gCg	p.E159A		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	159					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.E159A(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GAGAAGAGCGAGTTGGTGAAC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											160.0	117.0	132.0					22																	24580140		2203	4300	6503	SO:0001583	missense	56241			AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.476A>C	22.37:g.24580140A>C	ENSP00000351075:p.Glu159Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.808264	0.00606	.	.	ENSG00000099994	ENST00000358321	T	0.08008	3.14	3.6	1.33	0.21861	.	1.433850	0.04019	N	0.299396	T	0.05181	0.0138	N	0.19112	0.55	0.09310	N	1	B	0.22003	0.063	B	0.22386	0.039	T	0.34329	-0.9833	10	0.02654	T	1	-3.8408	5.014	0.14326	0.4509:0.3698:0.0:0.1793	.	159	Q9UGT4	SUSD2_HUMAN	A	159	ENSP00000351075:E159A	ENSP00000351075:E159A	E	+	2	0	SUSD2	22910140	0.002000	0.14202	0.034000	0.17996	0.002000	0.02628	0.729000	0.26028	0.114000	0.18032	-0.995000	0.02519	GAG		0.617	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1		NM_019601	
TGFBRAP1	9392	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	105886106	105886106	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr2:105886106C>A	ENST00000393359.2	-	11	2455	c.2029G>T	c.(2029-2031)Ggc>Tgc	p.G677C	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.G677C			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	677					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TCATGCTCGCCCAGCTTCCCG	0.647																																					Esophageal Squamous(183;794 2019 9730 21801 48859)												0													24.0	24.0	24.0					2																	105886106		2203	4300	6503	SO:0001583	missense	9392			AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2029G>T	2.37:g.105886106C>A	ENSP00000377027:p.Gly677Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.082580	0.76528	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.21932	1.98;1.98	5.54	4.64	0.57946	.	0.050983	0.85682	D	0.000000	T	0.49029	0.1533	M	0.81497	2.545	0.43421	D	0.995577	D;P	0.76494	0.999;0.732	D;P	0.71870	0.975;0.794	T	0.57021	-0.7882	10	0.72032	D	0.01	-18.1673	16.2274	0.82306	0.0:0.8668:0.1332:0.0	.	132;677	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	C	677;677;132	ENSP00000377027:G677C;ENSP00000258449:G677C	ENSP00000258449:G677C	G	-	1	0	TGFBRAP1	105252538	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	7.487000	0.81328	1.305000	0.44909	0.462000	0.41574	GGC		0.647	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2		NM_004257	
TP73	7161	hgsc.bcm.edu	37	1	3645988	3645989	+	Frame_Shift_Ins	INS	-	-	G	rs61736049|rs530995550	byFrequency	TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr1:3645988_3645989insG	ENST00000378295.4	+	10	1327_1328	c.1172_1173insG	c.(1171-1176)cagcagfs	p.Q392fs	TP73_ENST00000357733.3_Frame_Shift_Ins_p.Q392fs|TP73_ENST00000378290.4_Frame_Shift_Ins_p.Q321fs|TP73_ENST00000378285.1_Frame_Shift_Ins_p.Q343fs|TP73_ENST00000354437.4_Frame_Shift_Ins_p.Q392fs|TP73_ENST00000603362.1_Frame_Shift_Ins_p.Q392fs|TP73_ENST00000604479.1_Frame_Shift_Ins_p.Q392fs|TP73_ENST00000346387.4_Frame_Shift_Ins_p.Q392fs|TP73_ENST00000378280.1_Frame_Shift_Ins_p.Q343fs|TP73_ENST00000378288.4_Frame_Shift_Ins_p.Q343fs|TP73_ENST00000604074.1_Frame_Shift_Ins_p.Q392fs	NM_001204185.1|NM_005427.3	NP_001191114.1|NP_005418.1	O15350	P73_HUMAN	tumor protein p73	392	Poly-Gln.				activation of MAPK activity (GO:0000187)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|digestive tract morphogenesis (GO:0048546)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|hippocampus development (GO:0021766)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|kidney development (GO:0001822)|mismatch repair (GO:0006298)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell size (GO:0045793)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein tetramerization (GO:0051262)|release of cytochrome c from mitochondria (GO:0001836)|response to gamma radiation (GO:0010332)|response to organonitrogen compound (GO:0010243)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q391R(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|lung(8)|ovary(1)|prostate(1)	20	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)		TCCTATCGGCAGCAGCAGCAGC	0.609																																																	1	Substitution - Missense(1)	lung(1)																																								SO:0001589	frameshift_variant	7161			AB055065	CCDS49.1, CCDS44049.1, CCDS44050.1, CCDS44051.1, CCDS55566.1, CCDS55567.1, CCDS55568.1, CCDS55569.1, CCDS59965.1	1p36.3	2010-06-15			ENSG00000078900	ENSG00000078900			12003	protein-coding gene	gene with protein product		601990				9296498, 9288759	Standard	NM_001204186		Approved	P73	uc001akp.3	O15350	OTTHUMG00000000610	ENST00000378295.4:c.1173dupG	1.37:g.3645989_3645989dupG	ENSP00000367545:p.Gln392fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7J4|B7Z8Z1|B7Z9C1|C9J521|O15351|Q17RN8|Q5TBV5|Q5TBV6|Q8NHW9|Q8TDY5|Q8TDY6|Q9NTK8	Frame_Shift_Ins	INS	ENST00000378295.4	37	CCDS49.1																																																																																				0.609	TP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001468.4		NM_005427	
USP35	57558	hgsc.bcm.edu	37	11	77921393	77921402	+	Frame_Shift_Del	DEL	TGCTGCTCCG	TGCTGCTCCG	-	rs547090		TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	TGCTGCTCCG	TGCTGCTCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr11:77921393_77921402delTGCTGCTCCG	ENST00000529308.1	+	10	2753_2762	c.2492_2501delTGCTGCTCCG	c.(2491-2502)ctgctgctccgcfs	p.LLLR831fs	USP35_ENST00000530267.1_Frame_Shift_Del_p.LLLR399fs|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Frame_Shift_Del_p.LLLR562fs|USP35_ENST00000441408.2_Frame_Shift_Del_p.LLLR417fs	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	831	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			TCCATCCCCCTGCTGCTCCGCCTGCCACTG	0.624																																																	0																																										SO:0001589	frameshift_variant	57558			AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2492_2501delTGCTGCTCCG	11.37:g.77921393_77921402delTGCTGCTCCG	ENSP00000431876:p.Leu831fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000529308.1	37	CCDS41693.1																																																																																				0.624	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1		XM_290527	
KRTAP20-2	337976	broad.mit.edu;ucsc.edu	37	21	32007632	32007632	+	Missense_Mutation	SNP	T	T	G	rs8132721		TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr21:32007632T>G	ENST00000330798.2	+	1	78	c.50T>G	c.(49-51)gTc>gGc	p.V17G		NM_181616.1	NP_853647.1	Q3LI61	KR202_HUMAN	keratin associated protein 20-2	17			V -> G (in dbSNP:rs8132721).			intermediate filament (GO:0005882)		p.V17G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|ovary(1)	8						GGCTATGGAGTCCTGGGCGGT	0.537																																																	1	Substitution - Missense(1)	kidney(1)											197.0	159.0	172.0					21																	32007632		2203	4300	6503	SO:0001583	missense	337976			AP001708	CCDS13604.1	21q22.1	2006-03-13			ENSG00000184032	ENSG00000184032		"""Keratin associated proteins"""	18944	protein-coding gene	gene with protein product						12359730	Standard	NM_181616		Approved	KAP20.2	uc011adg.2	Q3LI61	OTTHUMG00000057786	ENST00000330798.2:c.50T>G	21.37:g.32007632T>G	ENSP00000330746:p.Val17Gly	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000330798.2	37	CCDS13604.1	.	.	.	.	.	.	.	.	.	.	G	3.806	-0.040607	0.07497	.	.	ENSG00000184032	ENST00000330798	T	0.06528	3.29	2.88	-0.109	0.13584	.	0.458821	0.15458	N	0.261281	T	0.04318	0.0119	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.87932	D	0	.	1.6402	0.02750	0.1142:0.1787:0.3416:0.3655	rs8132721;rs52833587;rs8132721	17	Q3LI61	KR202_HUMAN	G	17	ENSP00000330746:V17G	ENSP00000330746:V17G	V	+	2	0	KRTAP20-2	30929503	0.006000	0.16342	0.000000	0.03702	0.003000	0.03518	0.653000	0.24902	-0.294000	0.08973	-1.581000	0.00855	GTC		0.537	KRTAP20-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128238.3			
BAG4	9530	broad.mit.edu	37	8	38034599	38034599	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr8:38034599G>A	ENST00000287322.4	+	1	483	c.212G>A	c.(211-213)gGc>gAc	p.G71D	LSM1_ENST00000522515.1_5'Flank|LSM1_ENST00000311351.4_5'Flank|LSM1_ENST00000520755.1_5'Flank|BAG4_ENST00000432471.2_Missense_Mutation_p.G71D|BAG4_ENST00000521282.1_3'UTR	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	71					cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)	p.G71D(1)		breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				GGAGGCGATGGCTACTATCCC	0.701																																																	1	Substitution - Missense(1)	kidney(1)											17.0	16.0	17.0					8																	38034599		2199	4292	6491	SO:0001583	missense	9530			AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"""silencer of death domains"""	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.212G>A	8.37:g.38034599G>A	ENSP00000287322:p.Gly71Asp	Somatic		WXS	Illumina GAIIx	Phase_I	B4E217|O95818	Missense_Mutation	SNP	ENST00000287322.4	37	CCDS6104.1	.	.	.	.	.	.	.	.	.	.	G	34	5.329053	0.95733	.	.	ENSG00000156735	ENST00000432471;ENST00000287322	D;D	0.86432	-2.12;-1.82	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000013	D	0.91466	0.7306	M	0.63428	1.95	0.36744	D	0.882405	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.92733	0.6201	10	0.46703	T	0.11	-9.825	12.8495	0.57850	0.0:0.0:1.0:0.0	.	71;71	B4E217;O95429	.;BAG4_HUMAN	D	71	ENSP00000393298:G71D;ENSP00000287322:G71D	ENSP00000287322:G71D	G	+	2	0	BAG4	38153756	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.764000	0.47613	2.380000	0.81148	0.491000	0.48974	GGC		0.701	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2		NM_004874	
CDH24	64403	broad.mit.edu	37	14	23521190	23521190	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr14:23521190delC	ENST00000267383.5	-	8	1558	c.1466delG	c.(1465-1467)ggafs	p.G489fs	CDH24_ENST00000554034.1_Intron|CDH24_ENST00000487137.2_Intron|CDH24_ENST00000485922.1_5'Flank|CDH24_ENST00000397359.3_Frame_Shift_Del_p.G489fs			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	489	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TTGGGGGATTCCCACAGCGCT	0.627																																																	0													27.0	26.0	26.0					14																	23521190		2202	4293	6495	SO:0001589	frameshift_variant	64403			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.1466delG	14.37:g.23521190delC	ENSP00000267383:p.Gly489fs	Somatic		WXS	Illumina GAIIx	Phase_I	D3DS44|Q86UP1|Q9NT84	Frame_Shift_Del	DEL	ENST00000267383.5	37	CCDS9585.1																																																																																				0.627	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2		NM_022478	
DDX12P	440081	broad.mit.edu	37	12	9578354	9578354	+	IGR	SNP	A	A	C			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr12:9578354A>C								RP13-735L24.1 (28141 upstream) : SNORA75 (19299 downstream)																							AATTGCTGAAACCCAGCCAGT	0.597																																																	0													7.0	10.0	9.0					12																	9578354		685	1572	2257	SO:0001628	intergenic_variant	0																															12.37:g.9578354A>C		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.597									
NXPE3	91775	broad.mit.edu	37	3	101520532	101520532	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr3:101520532G>T	ENST00000491511.2	+	5	1503	c.547G>T	c.(547-549)Gta>Tta	p.V183L	NXPE3_ENST00000477909.1_Missense_Mutation_p.V183L|NXPE3_ENST00000273347.5_Missense_Mutation_p.V183L|NXPE3_ENST00000422132.1_Missense_Mutation_p.V183L	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	183						extracellular region (GO:0005576)		p.V183L(1)									CAAAGTTAAAGTATCCGTATC	0.493																																																	1	Substitution - Missense(1)	kidney(1)											81.0	84.0	83.0					3																	101520532		2203	4300	6503	SO:0001583	missense	0			AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.547G>T	3.37:g.101520532G>T	ENSP00000417485:p.Val183Leu	Somatic		WXS	Illumina GAIIx	Phase_I	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	37	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884435	0.91814	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	5.73	5.73	0.89815	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	T	0.31451	0.0797	L	0.42529	1.33	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.00277	-1.1854	10	0.26408	T	0.33	-14.1294	20.2602	0.98440	0.0:0.0:1.0:0.0	.	183	Q969Y0	FA55C_HUMAN	L	183	ENSP00000273347:V183L;ENSP00000417485:V183L;ENSP00000418369:V183L;ENSP00000396421:V183L	ENSP00000273347:V183L	V	+	1	0	FAM55C	103003222	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	7.926000	0.87569	2.861000	0.98227	0.655000	0.94253	GTA		0.493	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2		NM_145037	
LIN28A	79727	broad.mit.edu	37	1	26737960	26737960	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr1:26737960C>T	ENST00000326279.6	+	2	229	c.115C>T	c.(115-117)Cac>Tac	p.H39Y	LIN28A_ENST00000254231.4_Missense_Mutation_p.H39Y	NM_024674.4	NP_078950.1	Q9H9Z2	LN28A_HUMAN	lin-28 homolog A (C. elegans)	39	CSD.				germ cell development (GO:0007281)|miRNA catabolic process (GO:0010587)|negative regulation of glial cell differentiation (GO:0045686)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of translation (GO:0045727)|pre-miRNA processing (GO:0031054)|regulation of gene silencing by miRNA (GO:0060964)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)	8						TCAGCTGCTGCACGGTGCGGG	0.721																																																	0													24.0	28.0	26.0					1																	26737960		2200	4298	6498	SO:0001583	missense	79727			AF521099	CCDS280.1	1p35.3	2013-01-09	2010-04-06	2010-04-06	ENSG00000131914	ENSG00000131914		"""Zinc fingers, CCHC domain containing"""	15986	protein-coding gene	gene with protein product		611043	"""lin-28 homolog (C. elegans)"""	LIN28		12798299	Standard	XM_006710899		Approved	LIN-28, FLJ12457, ZCCHC1, CSDD1	uc001bmj.3	Q9H9Z2	OTTHUMG00000003550	ENST00000326279.6:c.115C>T	1.37:g.26737960C>T	ENSP00000363314:p.His39Tyr	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000326279.6	37	CCDS280.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469821	0.43839	.	.	ENSG00000131914	ENST00000326279;ENST00000254231	T;T	0.43294	0.95;0.95	5.95	5.95	0.96441	Nucleic acid-binding, OB-fold-like (1);	0.064055	0.64402	D	0.000013	T	0.28863	0.0716	N	0.14661	0.345	0.35086	D	0.763851	D	0.54207	0.965	B	0.37833	0.259	T	0.42137	-0.9469	10	0.59425	D	0.04	.	19.0218	0.92919	0.0:1.0:0.0:0.0	.	39	Q9H9Z2	LN28A_HUMAN	Y	39	ENSP00000363314:H39Y;ENSP00000254231:H39Y	ENSP00000254231:H39Y	H	+	1	0	LIN28A	26610547	1.000000	0.71417	1.000000	0.80357	0.138000	0.21146	5.102000	0.64572	2.835000	0.97688	0.650000	0.86243	CAC		0.721	LIN28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009891.2		NM_024674	
TMPRSS6	164656	broad.mit.edu	37	22	37480371	37480371	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr22:37480371G>T	ENST00000346753.3	-	10	1303	c.1187C>A	c.(1186-1188)cCg>cAg	p.P396Q	TMPRSS6_ENST00000381792.2_Missense_Mutation_p.P387Q|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.P387Q|RP5-1170K4.7_ENST00000414203.2_RNA|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.P396Q|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.P387Q	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	396	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CTGGGTGCACGGCAAATCATA	0.607																																																	0													142.0	90.0	108.0					22																	37480371		2203	4300	6503	SO:0001583	missense	164656			AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1187C>A	22.37:g.37480371G>T	ENSP00000334962:p.Pro396Gln	Somatic		WXS	Illumina GAIIx	Phase_I	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	G	1.791	-0.479535	0.04383	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000429068;ENST00000442782	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	4.57	1.3	0.21679	CUB (4);	0.568125	0.17459	N	0.173511	T	0.27134	0.0665	L	0.51422	1.61	0.09310	N	0.999992	D;D;P	0.64830	0.994;0.969;0.819	P;P;B	0.55615	0.78;0.54;0.339	T	0.08785	-1.0705	10	0.30854	T	0.27	.	7.7129	0.28688	0.2856:0.0:0.7144:0.0	.	396;387;396	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	Q	387;396;387;387;58;396	ENSP00000371211:P387Q;ENSP00000334962:P396Q;ENSP00000385453:P387Q;ENSP00000384964:P387Q;ENSP00000392433:P58Q;ENSP00000397691:P396Q	ENSP00000334962:P396Q	P	-	2	0	TMPRSS6	35810317	1.000000	0.71417	0.006000	0.13384	0.097000	0.18754	3.710000	0.54860	0.345000	0.23873	0.591000	0.81541	CCG		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1		NM_153609	
PRSS3P2	154754	broad.mit.edu	37	7	142481271	142481271	+	RNA	SNP	A	A	C			TCGA-B8-4620-01A-01D-1553-08	TCGA-B8-4620-11A-01D-1553-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69686924-5a9f-4e07-9e6d-62a3435f9971	eb4eb312-f11f-4a33-bf85-bb0d4a294c54	g.chr7:142481271A>C	ENST00000603901.1	+	0	345					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										AGCTCTCCACACCTGCCGTCA	0.537																																																	0													215.0	146.0	168.0					7																	142481271		684	1496	2180			0					7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142481271A>C		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000603901.1	37																																																																																					0.537	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1		NR_001296	
