#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
ADCY2	108	hgsc.bcm.edu	37	5	7757684	7757715	+	Splice_Site	DEL	GGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	GGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	-	rs138503341|rs376428226|rs4072341|rs375816730|rs4479814	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	GGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	GGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr5:7757684_7757715delGGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	ENST00000338316.4	+	16	2168_2183	c.2079_2094delGGCCGTGTTCAACATGGTAAGTCCCAGAGCAC	c.(2077-2094)atggccgtgttcaacatg>at	p.MAVFNM693fs	ADCY2_ENST00000537121.1_Splice_Site_p.MAVFNM513fs	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	693					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.?(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TATTAATGATGGCCGTGTTCAACATGGTAAGTCCCAGAGCACGGCCGTGTTC	0.547																																																	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)																																								SO:0001630	splice_region_variant	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2094+1GGCCGTGTTCAACATGGTAAGTCCCAGAGCAC>-	5.37:g.7757684_7757715delGGCCGTGTTCAACATGGTAAGTCCCAGAGCAC		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Frame_Shift_Del	DEL	ENST00000338316.4	37	CCDS3872.2																																																																																				0.547	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2		NM_020546	Frame_Shift_Del
AIM1L	55057	hgsc.bcm.edu	37	1	26673138	26673139	+	5'Flank	INS	-	-	CCT	rs141177722	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr1:26673138_26673139insCCT	ENST00000308182.5	-	0	0				AIM1L_ENST00000527815.1_5'Flank|RN7SL490P_ENST00000579210.1_RNA			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		GGGCCCACCTGCCTCCTCCATG	0.614														74	0.0147764	0.0537	0.0029	5008	,	,		17019	0.0		0.001	False		,,,				2504	0.0																0										143,3425		28,87,1669						5.3	1.0		dbSNP_134	7	1,7697		0,1,3848	no	coding	AIM1L	NM_001039775.3		28,88,5517	A1A1,A1R,RR		0.013,4.0078,1.2782				144,11122				SO:0001631	upstream_gene_variant	55057					1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673142_26673144dupCCT	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNG3|Q5T137|Q5T150	In_Frame_Ins	INS	ENST00000308182.5	37																																																																																					0.614	AIM1L-201	KNOWN	basic	protein_coding	protein_coding			NM_001039775.2	
AKAP1	8165	hgsc.bcm.edu	37	17	55183771	55183771	+	Missense_Mutation	SNP	G	G	A	rs138803240		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr17:55183771G>A	ENST00000337714.3	+	2	1179	c.946G>A	c.(946-948)Ggc>Agc	p.G316S	AKAP1_ENST00000314126.3_Missense_Mutation_p.G316S|AKAP1_ENST00000539273.1_Missense_Mutation_p.G316S|AKAP1_ENST00000571629.1_Missense_Mutation_p.G316S|AKAP1_ENST00000572557.1_Missense_Mutation_p.G316S	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	316					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G316S(1)		endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					AAATGAGGAGGGCTTGGATAG	0.537																																																	1	Substitution - Missense(1)	ovary(1)											90.0	97.0	95.0					17																	55183771		2203	4300	6503	SO:0001583	missense	8165			X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.946G>A	17.37:g.55183771G>A	ENSP00000337736:p.Gly316Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	5.256	0.232698	0.09969	.	.	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.32023	1.47;1.98;1.47	2.7	-1.29	0.09288	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32798	-0.9893	9	0.20046	T	0.44	.	7.7099	0.28671	0.4984:0.0:0.5016:0.0	.	316	Q92667	AKAP1_HUMAN	S	316;316;358;316	ENSP00000337736:G316S;ENSP00000314075:G316S;ENSP00000443139:G316S	ENSP00000314075:G316S	G	+	1	0	AKAP1	52538770	0.304000	0.24472	0.000000	0.03702	0.109000	0.19521	-2.009000	0.01455	-0.456000	0.07043	-1.328000	0.01277	GGC		0.537	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			
CAST	831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	96103643	96103644	+	Missense_Mutation	DNP	TC	TC	CT	rs572539750		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr5:96103643_96103644TC>CT	ENST00000341926.3	+	27	2121_2122	c.1959_1960TC>CT	c.(1957-1962)gcTCtc>gcCTtc	p.L654F	CAST_ENST00000508608.1_Missense_Mutation_p.L700F|CAST_ENST00000504465.1_Missense_Mutation_p.L582F|CAST_ENST00000325674.7_Missense_Mutation_p.L702F|CAST_ENST00000395812.2_Missense_Mutation_p.L696F|CAST_ENST00000511049.1_Missense_Mutation_p.L639F|CAST_ENST00000309190.5_Missense_Mutation_p.L632F|CAST_ENST00000510756.1_Missense_Mutation_p.L715F|CAST_ENST00000511782.1_Missense_Mutation_p.L640F|ERAP1_ENST00000296754.3_Intron|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000508830.1_Missense_Mutation_p.L737F|CAST_ENST00000515663.1_Missense_Mutation_p.L377F|CAST_ENST00000359176.4_Missense_Mutation_p.L718F|CAST_ENST00000509903.1_Missense_Mutation_p.L619F|CAST_ENST00000395813.1_Missense_Mutation_p.L737F|CAST_ENST00000338252.3_Missense_Mutation_p.L641F|CAST_ENST00000508579.1_Missense_Mutation_p.L369F			P20810	ICAL_HUMAN	calpastatin	654					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)	p.L632F(1)|p.A631A(1)		breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CCATTGATGCTCTCTCAGGAGA	0.441																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)																																								SO:0001583	missense	831			AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	Exception_encountered	5.37:g.96103643_96103644delinsCT	ENSP00000339914:p.Leu654Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Silent|Missense_Mutation	SNP	ENST00000341926.3	37																																																																																					0.441	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2		NM_173062	
CD200R1	131450	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	112647851	112647851	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr3:112647851G>A	ENST00000471858.1	-	4	744	c.512C>T	c.(511-513)gCa>gTa	p.A171V	CD200R1_ENST00000440122.2_3'UTR|CD200R1_ENST00000490004.1_3'UTR|CD200R1_ENST00000295863.4_Missense_Mutation_p.A149V|CD200R1_ENST00000308611.3_Missense_Mutation_p.A194V	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	171	Ig-like C2-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.A194V(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGGCTTCCCTGCAACTGCCTT	0.478																																																	1	Substitution - Missense(1)	kidney(1)											92.0	79.0	83.0					3																	112647851		2203	4300	6503	SO:0001583	missense	131450			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.512C>T	3.37:g.112647851G>A	ENSP00000418928:p.Ala171Val	Somatic		WXS	Illumina HiSeq	Phase_I	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805248	0.50315	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863	T;T;T	0.44881	0.91;0.91;6.22	5.43	4.55	0.56014	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389670	0.24762	N	0.035802	T	0.55289	0.1911	M	0.68317	2.08	0.80722	D	1	P;D;D	0.61697	0.932;0.99;0.987	P;P;P	0.61328	0.725;0.887;0.82	T	0.50558	-0.8814	10	0.32370	T	0.25	.	10.7456	0.46179	0.0892:0.0:0.9108:0.0	.	149;171;194	B4E2U2;Q8TD46;Q8TD46-4	.;MO2R1_HUMAN;.	V	171;194;149	ENSP00000418928:A171V;ENSP00000311035:A194V;ENSP00000295863:A149V	ENSP00000295863:A149V	A	-	2	0	CD200R1	114130541	0.042000	0.20092	0.945000	0.38365	0.542000	0.35054	0.940000	0.28992	2.538000	0.85594	0.650000	0.86243	GCA		0.478	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1		NM_138806	
COL14A1	7373	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	121282409	121282409	+	Missense_Mutation	SNP	C	C	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr8:121282409C>A	ENST00000297848.3	+	26	3479	c.3209C>A	c.(3208-3210)aCc>aAc	p.T1070N	COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.T975N|COL14A1_ENST00000309791.4_Missense_Mutation_p.T1070N	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.T1070N(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ACAGATGGAACCCAAGTAAGG	0.373																																																	1	Substitution - Missense(1)	kidney(1)											66.0	64.0	64.0					8																	121282409		2203	4299	6502	SO:0001583	missense	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3209C>A	8.37:g.121282409C>A	ENSP00000297848:p.Thr1070Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678581	0.88542	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781	D;D;D	0.84730	-1.89;-1.89;-1.89	5.21	5.21	0.72293	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.94308	0.8171	M	0.93016	3.37	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94547	0.7750	10	0.51188	T	0.08	.	18.9528	0.92646	0.0:1.0:0.0:0.0	.	1070	Q05707	COEA1_HUMAN	N	1070;1070;975	ENSP00000311809:T1070N;ENSP00000297848:T1070N;ENSP00000247781:T975N	ENSP00000247781:T975N	T	+	2	0	COL14A1	121351590	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.809000	0.62591	2.716000	0.92895	0.561000	0.74099	ACC		0.373	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2		NM_021110	
DNAH8	1769	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	38942198	38942198	+	Missense_Mutation	SNP	T	T	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr6:38942198T>G	ENST00000359357.3	+	83	12330	c.12076T>G	c.(12076-12078)Ttg>Gtg	p.L4026V	DNAH8_ENST00000441566.1_Missense_Mutation_p.L3990V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4026	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L4026V(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACGCGCAGGTTTGAAAAGAAC	0.383																																																	2	Substitution - Missense(2)	kidney(2)											82.0	75.0	77.0					6																	38942198		2203	4300	6503	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12076T>G	6.37:g.38942198T>G	ENSP00000352312:p.Leu4026Val	Somatic		WXS	Illumina HiSeq	Phase_I	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	T	19.70	3.876432	0.72180	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.14391	2.51;2.51;2.51	5.84	1.84	0.25277	Dynein heavy chain (1);	0.000000	0.64402	D	0.000008	T	0.23649	0.0572	M	0.87827	2.91	0.45390	D	0.998372	D;D	0.61697	0.987;0.99	P;P	0.62491	0.843;0.903	T	0.04976	-1.0914	10	0.66056	D	0.02	.	9.461	0.38785	0.0:0.3535:0.0:0.6465	.	3990;4026	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	V	4231;4026;3990	ENSP00000333363:L4231V;ENSP00000352312:L4026V;ENSP00000402294:L3990V	ENSP00000333363:L4231V	L	+	1	2	DNAH8	39050176	0.105000	0.21958	0.769000	0.31535	0.989000	0.77384	0.432000	0.21461	0.358000	0.24211	0.533000	0.62120	TTG		0.383	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1		NM_001206927	
FAM131C	348487	hgsc.bcm.edu	37	1	16386008	16386008	+	Silent	SNP	T	T	C	rs2863452	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr1:16386008T>C	ENST00000375662.4	-	6	726	c.543A>G	c.(541-543)caA>caG	p.Q181Q	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	181										large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGACGATGCCTTGGGGGCTGT	0.642													C|||	3614	0.721645	0.5061	0.7709	5008	,	,		13138	0.8343		0.7654	False		,,,				2504	0.817																0													28.0	25.0	26.0					1																	16386008		1930	4122	6052	SO:0001819	synonymous_variant	348487				CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.543A>G	1.37:g.16386008T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																				0.642	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1		NM_182623	
GOLGA3	2802	broad.mit.edu;ucsc.edu	37	12	133374959	133374959	+	Missense_Mutation	SNP	C	C	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr12:133374959C>G	ENST00000450791.2	-	8	2088	c.1905G>C	c.(1903-1905)aaG>aaC	p.K635N	GOLGA3_ENST00000204726.3_Missense_Mutation_p.K635N|GOLGA3_ENST00000537452.1_Missense_Mutation_p.K635N|GOLGA3_ENST00000545875.1_Missense_Mutation_p.K635N|GOLGA3_ENST00000456883.2_Missense_Mutation_p.K635N			Q08378	GOGA3_HUMAN	golgin A3	635	Gln-rich.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.K635N(2)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CGATGCGCCCCTTCTCCTTCA	0.592																																																	2	Substitution - Missense(2)	kidney(2)											113.0	102.0	106.0					12																	133374959		2203	4300	6503	SO:0001583	missense	2802			AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.1905G>C	12.37:g.133374959C>G	ENSP00000410378:p.Lys635Asn	Somatic		WXS	Illumina GAIIx	Phase_I	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.529837	0.45073	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.64438	0.37;0.37;0.34;-0.1;-0.1	5.8	2.98	0.34508	.	0.000000	0.85682	D	0.000000	T	0.68476	0.3005	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.70128	-0.4957	10	0.87932	D	0	.	14.1721	0.65517	0.0:0.8607:0.0:0.1393	.	635;635;635	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	N	635	ENSP00000204726:K635N;ENSP00000410378:K635N;ENSP00000409303:K635N;ENSP00000442143:K635N;ENSP00000442603:K635N	ENSP00000204726:K635N	K	-	3	2	GOLGA3	131885032	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	0.837000	0.27558	0.362000	0.24319	-0.940000	0.02684	AAG		0.592	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2		NM_005895	
IGSF22	283284	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	18729752	18729752	+	Splice_Site	SNP	A	A	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr11:18729752A>G	ENST00000513874.1	-	19	3227		c.e19+1		IGSF22_ENST00000510673.1_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22									p.?(1)		NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						GGGACAACTCACAGAGAAGGC	0.552																																																	1	Unknown(1)	kidney(1)											139.0	134.0	135.0					11																	18729752		692	1591	2283	SO:0001630	splice_region_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.3087+1T>C	11.37:g.18729752A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NNA0|D6RGV7	Splice_Site	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	A	13.95	2.391246	0.42410	.	.	ENSG00000179057	ENST00000513874	.	.	.	4.11	4.11	0.48088	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1102	0.53836	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IGSF22	18686328	0.984000	0.35163	0.993000	0.49108	0.521000	0.34408	2.654000	0.46699	1.846000	0.53633	0.528000	0.53228	.		0.552	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2		NM_173588	Intron
KRT3	3850	hgsc.bcm.edu	37	12	53189428	53189428	+	Silent	SNP	C	C	A	rs148531142|rs184322044		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr12:53189428C>A	ENST00000417996.2	-	1	473	c.399G>T	c.(397-399)ggG>ggT	p.G133G	KRT3_ENST00000309505.3_Silent_p.G133G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	133	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						agccaccagcccctccaaagc	0.632																																																	0													141.0	187.0	172.0					12																	53189428		2177	4259	6436	SO:0001819	synonymous_variant	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.399G>T	12.37:g.53189428C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																				0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1		NM_057088	
KRT3	3850	hgsc.bcm.edu	37	12	53189446	53189446	+	Silent	SNP	C	C	T	rs117364830	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr12:53189446C>T	ENST00000417996.2	-	1	455	c.381G>A	c.(379-381)ggG>ggA	p.G127G	KRT3_ENST00000309505.3_Silent_p.G127G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	127	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						agccaccagcccctccaaagc	0.632																																																	0													148.0	189.0	175.0					12																	53189446		2189	4287	6476	SO:0001819	synonymous_variant	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.381G>A	12.37:g.53189446C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																				0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1		NM_057088	
MUC4	4585	hgsc.bcm.edu	37	3	195508452	195508452	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr3:195508452G>T	ENST00000463781.3	-	2	10458	c.9999C>A	c.(9997-9999)agC>agA	p.S3333R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3333R	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGGGCTGGTGACAT	0.592																																																	1	Deletion - In frame(1)	stomach(1)											28.0	22.0	24.0					3																	195508452		689	1572	2261	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9999C>A	3.37:g.195508452G>T	ENSP00000417498:p.Ser3333Arg	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.009	0.187267	0.09547	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.49;1.46	0.423	0.423	0.16463	.	.	.	.	.	T	0.17195	0.0413	N	0.08118	0	0.09310	N	1	P	0.42993	0.797	P	0.45558	0.485	T	0.17623	-1.0363	7	.	.	.	.	.	.	.	.	3205	E7ESK3	.	R	3333	ENSP00000417498:S3333R;ENSP00000420243:S3333R	.	S	-	3	2	MUC4	196993231	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-2.928000	0.00690	0.494000	0.27859	0.089000	0.15464	AGC		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
NEUROD2	4761	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	37762561	37762561	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr17:37762561C>T	ENST00000302584.4	-	2	512	c.292G>A	c.(292-294)Ggc>Agc	p.G98S		NM_006160.3	NP_006151.3	Q15784	NDF2_HUMAN	neuronal differentiation 2	98					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|cellular response to calcium ion (GO:0071277)|cellular response to electrical stimulus (GO:0071257)|cerebellar cortex development (GO:0021695)|negative regulation of synapse maturation (GO:2000297)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.G98S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)			GGCCGCTCGCCCTCCGCCTCG	0.687																																																	1	Substitution - Missense(1)	kidney(1)											33.0	27.0	29.0					17																	37762561		2203	4300	6503	SO:0001583	missense	4761			U58681	CCDS11338.1	17q12	2013-05-21	2012-02-22		ENSG00000171532	ENSG00000171532		"""Basic helix-loop-helix proteins"""	7763	protein-coding gene	gene with protein product		601725	"""neurogenic differentiation 2"""			9119405	Standard	XM_005257409		Approved	NDRF, bHLHa1	uc002hry.3	Q15784	OTTHUMG00000133211	ENST00000302584.4:c.292G>A	17.37:g.37762561C>T	ENSP00000306754:p.Gly98Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TBI7|Q9UQC6	Missense_Mutation	SNP	ENST00000302584.4	37	CCDS11338.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.105971	0.77096	.	.	ENSG00000171532	ENST00000302584	D	0.96745	-4.11	5.25	5.25	0.73442	.	0.128312	0.51477	U	0.000086	D	0.96213	0.8765	L	0.49126	1.545	0.54753	D	0.999985	D	0.56968	0.978	P	0.54759	0.76	D	0.94800	0.7970	10	0.21540	T	0.41	-7.2286	17.6108	0.88053	0.0:1.0:0.0:0.0	.	98	Q15784	NDF2_HUMAN	S	98	ENSP00000306754:G98S	ENSP00000306754:G98S	G	-	1	0	NEUROD2	35016087	0.935000	0.31712	1.000000	0.80357	0.988000	0.76386	4.789000	0.62446	2.451000	0.82905	0.511000	0.50034	GGC		0.687	NEUROD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256931.2		NM_006160	
PCLO	27445	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	82582250	82582250	+	Missense_Mutation	SNP	T	T	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr7:82582250T>G	ENST00000333891.9	-	5	8356	c.8019A>C	c.(8017-8019)gaA>gaC	p.E2673D	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.E2673D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.E2673D(2)|p.E2604D(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTTGGAAACTTCAGTAGTGA	0.458																																																	3	Substitution - Missense(3)	kidney(3)											75.0	74.0	75.0					7																	82582250		1898	4119	6017	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8019A>C	7.37:g.82582250T>G	ENSP00000334319:p.Glu2673Asp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	5.813	0.334275	0.11013	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.18960	2.18;2.19	5.36	1.36	0.22044	.	.	.	.	.	T	0.13200	0.0320	L	0.34521	1.04	0.80722	D	1	B;B	0.14805	0.006;0.011	B;B	0.19946	0.007;0.027	T	0.16897	-1.0387	9	0.87932	D	0	.	1.6109	0.02693	0.1251:0.1545:0.2342:0.4863	.	2673;2673	Q9Y6V0-5;Q9Y6V0-6	.;.	D	2604;2673;2673	ENSP00000334319:E2673D;ENSP00000388393:E2673D	ENSP00000334319:E2673D	E	-	3	2	PCLO	82420186	0.432000	0.25554	0.007000	0.13788	0.661000	0.39034	0.248000	0.18198	0.327000	0.23409	0.482000	0.46254	GAA		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5		NM_014510	
SCAF1	58506	hgsc.bcm.edu	37	19	50154270	50154271	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr19:50154270_50154271insC	ENST00000360565.3	+	7	748_749	c.624_625insC	c.(625-627)cccfs	p.P209fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	209	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		ccccttcccctcccccaccccc	0.703																																																	0																																										SO:0001589	frameshift_variant	58506			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.629dupC	19.37:g.50154275_50154275dupC	ENSP00000353769:p.Pro209fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Ins	INS	ENST00000360565.3	37	CCDS33074.1																																																																																				0.703	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1		NM_021228	
TGFBRAP1	9392	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	105915065	105915065	+	Silent	SNP	C	C	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr2:105915065C>T	ENST00000393359.2	-	3	1212	c.786G>A	c.(784-786)gcG>gcA	p.A262A	TGFBRAP1_ENST00000258449.1_Silent_p.A262A			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	262	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				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)	p.A262A(1)		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						CGTCATCGAGCGCTATGACGT	0.542																																					Esophageal Squamous(183;794 2019 9730 21801 48859)												1	Substitution - coding silent(1)	kidney(1)											106.0	96.0	99.0					2																	105915065		2203	4300	6503	SO:0001819	synonymous_variant	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.786G>A	2.37:g.105915065C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																				0.542	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2		NM_004257	
STEAP3	55240	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	120012306	120012306	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr2:120012306G>A	ENST00000354888.5	+	5	1571	c.1067G>A	c.(1066-1068)cGg>cAg	p.R356Q	STEAP3_ENST00000450943.2_Missense_Mutation_p.R356Q|STEAP3_ENST00000393106.2_Missense_Mutation_p.R356Q|STEAP3_ENST00000409811.1_Missense_Mutation_p.R356Q|STEAP3_ENST00000393108.2_Missense_Mutation_p.R356Q|STEAP3_ENST00000393110.2_Missense_Mutation_p.R366Q|STEAP3_ENST00000425223.2_Missense_Mutation_p.R356Q|STEAP3_ENST00000393107.2_Missense_Mutation_p.R356Q	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	356	Ferric oxidoreductase.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)	p.R356Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						GAGGTCTGGCGGATGGAGATC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											122.0	109.0	114.0					2																	120012306		2203	4300	6503	SO:0001583	missense	55240			AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.1067G>A	2.37:g.120012306G>A	ENSP00000346961:p.Arg356Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Missense_Mutation	SNP	ENST00000354888.5	37	CCDS2125.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.046299	0.93740	.	.	ENSG00000115107	ENST00000393108;ENST00000354888;ENST00000450943;ENST00000393110;ENST00000393106;ENST00000409811;ENST00000393107;ENST00000425223	D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	5.29	5.29	0.74685	Flavoprotein transmembrane component (1);	0.000000	0.85682	D	0.000000	D	0.94843	0.8334	M	0.71206	2.165	0.47123	D	0.999327	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.946	D	0.94080	0.7343	9	.	.	.	-34.8103	18.0968	0.89493	0.0:0.0:1.0:0.0	.	356;366;356	B8ZZX6;Q658P3-2;Q658P3	.;.;STEA3_HUMAN	Q	356;356;356;366;356;356;356;356	ENSP00000376820:R356Q;ENSP00000346961:R356Q;ENSP00000396873:R356Q;ENSP00000376822:R366Q;ENSP00000376818:R356Q;ENSP00000386510:R356Q;ENSP00000376819:R356Q;ENSP00000396214:R356Q	.	R	+	2	0	STEAP3	119728776	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	6.647000	0.74354	2.756000	0.94617	0.561000	0.74099	CGG		0.607	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1		NM_018234	
FAM92A1P2	403315	broad.mit.edu	37	4	183960484	183960484	+	RNA	DEL	A	A	-	rs542231248		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr4:183960484delA	ENST00000502308.1	+	0	1667					NR_003612.1				family with sequence similarity 92, member A1 pseudogene 2																		TTCAACATCCAAAAAAAAAAA	0.308																																																	0																																												0			BC022019		4q35.1	2012-04-19	2012-04-19	2012-04-19	ENSG00000230219	ENSG00000230219			32287	pseudogene	pseudogene			"""family with sequence similarity 92, member A3"""	FAM92A3		12477932	Standard	NR_003612		Approved	MGC71735, MGC102964	uc003ivi.4		OTTHUMG00000160675		4.37:g.183960484delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000502308.1	37																																																																																					0.308	FAM92A1P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361814.1			
HPS4	89781	broad.mit.edu	37	22	26853885	26853885	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr22:26853885G>T	ENST00000398145.2	-	13	2511	c.1895C>A	c.(1894-1896)gCc>gAc	p.A632D	HPS4_ENST00000398141.1_Missense_Mutation_p.A645D|HPS4_ENST00000336873.5_Missense_Mutation_p.A632D|HPS4_ENST00000493455.2_5'UTR|HPS4_ENST00000402105.3_Missense_Mutation_p.A627D	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	632					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)	p.A645D(2)|p.A632D(2)		breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						CAGGCTGACGGCCTGGAGGAA	0.592									Hermansky-Pudlak syndrome																																								4	Substitution - Missense(4)	prostate(2)|kidney(2)											53.0	51.0	51.0					22																	26853885		2203	4300	6503	SO:0001583	missense	89781	Familial Cancer Database	HPS, HPS1-8		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.1895C>A	22.37:g.26853885G>T	ENSP00000381213:p.Ala632Asp	Somatic		WXS	Illumina GAIIx	Phase_I	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	37	CCDS13835.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778402	0.90195	.	.	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.53238	0.1784	M	0.77103	2.36	0.46564	D	0.9991	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999	T	0.58470	-0.7631	10	0.87932	D	0	-23.3461	16.0907	0.81088	0.0:0.0:1.0:0.0	.	632;632;632;645;627	Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;HPS4_HUMAN;.;.;.	D	632;645;627;632	ENSP00000381213:A632D;ENSP00000381210:A645D;ENSP00000384185:A627D;ENSP00000338457:A632D	ENSP00000338457:A632D	A	-	2	0	HPS4	25183885	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.216000	0.72212	2.390000	0.81377	0.655000	0.94253	GCC		0.592	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1		NM_022081	
RPAP1	26015	broad.mit.edu	37	15	41815547	41815547	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr15:41815547G>T	ENST00000304330.4	-	18	2558	c.2442C>A	c.(2440-2442)agC>agA	p.S814R	RPAP1_ENST00000561603.1_Missense_Mutation_p.S814R	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	814						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.S814R(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCGGGCATGAGCTTGGCTGGT	0.602																																																	1	Substitution - Missense(1)	kidney(1)											32.0	33.0	33.0					15																	41815547		2203	4300	6503	SO:0001583	missense	26015			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2442C>A	15.37:g.41815547G>T	ENSP00000306123:p.Ser814Arg	Somatic		WXS	Illumina GAIIx	Phase_I	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	G	5.456	0.269185	0.10349	.	.	ENSG00000103932	ENST00000304330	T	0.63255	-0.03	5.7	2.51	0.30379	.	1.417960	0.03651	N	0.240958	T	0.54095	0.1837	L	0.39898	1.24	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.42649	-0.9439	10	0.59425	D	0.04	-18.453	5.0396	0.14452	0.0874:0.1561:0.6145:0.1419	.	814	Q9BWH6	RPAP1_HUMAN	R	814	ENSP00000306123:S814R	ENSP00000306123:S814R	S	-	3	2	RPAP1	39602839	0.000000	0.05858	0.009000	0.14445	0.010000	0.07245	0.061000	0.14366	0.719000	0.32188	0.655000	0.94253	AGC		0.602	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2		NM_015540	
CDR2	1039	broad.mit.edu	37	16	22444123	22444123	+	5'UTR	SNP	G	G	A	rs200715642		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr16:22444123G>A	ENST00000569045.1	-	0	509				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)		ATCACTATCCGCTCAAAATTC	0.333																																																	0																																										SO:0001623	5_prime_UTR_variant	100131998			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		ENST00000569045.1:c.-317C>T	16.37:g.22444123G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A8K8A8|Q13977	RNA	SNP	ENST00000569045.1	37																																																																																					0.333	CDR2-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000430087.1			
SUSD2	56241	broad.mit.edu	37	22	24577515	24577517	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr22:24577515_24577517delCTG	ENST00000358321.3	+	1	289_291	c.28_30delCTG	c.(28-30)ctgdel	p.L13del		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	13					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)			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						GCCCTGGGCCCTGCTGCTGCTGG	0.685																																																	0																																										SO:0001651	inframe_deletion	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.28_30delCTG	22.37:g.24577524_24577526delCTG	ENSP00000351075:p.Leu13del	Somatic		WXS	Illumina GAIIx	Phase_I	Q9H5Y6	In_Frame_Del	DEL	ENST00000358321.3	37	CCDS13824.1																																																																																				0.685	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1		NM_019601	
TPTE2P3	220115	broad.mit.edu	37	13	53151275	53151275	+	IGR	DEL	C	C	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr13:53151275delC								RP11-78J21.4 (77835 upstream) : HNRNPA1L2 (40329 downstream)																							AAGAAAAACACTGTTTATAAA	0.368																																																	0																																										SO:0001628	intergenic_variant	220115																															13.37:g.53151275delC		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.368									
LOC149351	149351	broad.mit.edu	37	1	91296515	91296515	+	lincRNA	DEL	A	A	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e3f75b12-27ee-4d38-bd72-f6e167a25da6	14556f56-ec45-48fe-96ef-cd4ff64ec294	g.chr1:91296515delA	ENST00000435649.2	-	0	300																											TCAAGAGGGGAAAAAAAGTCT	0.383																																																	0																																												0																															1.37:g.91296515delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000435649.2	37																																																																																					0.383	RP4-665J23.1-004	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470185.1			
