#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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AK9	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000368948.2_In_Frame_Del_p.E703del|AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	703					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTTACCTTGCTTCTTCTTCTTC	0.227														1863	0.372005	0.2542	0.4092	5008	,	,		14640	0.377		0.4095	False		,,,				2504	0.4611																0										396,1116		113,170,473						-0.1	0.2		dbSNP_130	6	1116,1910		355,406,752	no	coding	AKD1	NM_001145128.2		468,576,1225	A1A1,A1R,RR		36.8804,26.1905,33.3186				1512,3026				SO:0001651	inframe_deletion	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2108_2110delAAG	6.37:g.109906339_109906341delCTT	ENSP00000410186:p.Glu703del		A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	In_Frame_Del	DEL	ENST00000424296.2	37	CCDS55048.1																																																																																				0.227	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001145128	
ASAP2	8853	hgsc.bcm.edu	37	2	9543400	9543400	+	Missense_Mutation	SNP	G	G	C			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr2:9543400G>C	ENST00000281419.3	+	28	3305	c.2965G>C	c.(2965-2967)Gat>Cat	p.D989H	ASAP2_ENST00000315273.4_Missense_Mutation_p.D944H	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	989	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CATTGATGGAGATCCTGGTCG	0.408																																																	0													139.0	125.0	130.0					2																	9543400		2203	4299	6502	SO:0001583	missense	8853			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2965G>C	2.37:g.9543400G>C	ENSP00000281419:p.Asp989His		D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.326616	0.60743	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.57907	1.48;0.37	5.86	5.86	0.93980	Src homology-3 domain (4);	0.181068	0.53938	D	0.000051	T	0.63861	0.2547	L	0.52126	1.63	0.53005	D	0.999967	P;B	0.46220	0.874;0.004	P;B	0.53593	0.73;0.031	T	0.59156	-0.7507	10	0.42905	T	0.14	.	20.1864	0.98220	0.0:0.0:1.0:0.0	.	944;989	O43150-2;O43150	.;ASAP2_HUMAN	H	989;944	ENSP00000281419:D989H;ENSP00000316404:D944H	ENSP00000281419:D989H	D	+	1	0	ASAP2	9460851	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	9.405000	0.97313	2.781000	0.95711	0.650000	0.86243	GAT		0.408	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1		NM_003887	
NCOR1P1	149934	hgsc.bcm.edu	37	20	26084228	26084228	+	RNA	SNP	G	G	A	rs75212180	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr20:26084228G>A	ENST00000478176.1	-	0	229					NR_003678.1		Q9H4R4	CT191_HUMAN	nuclear receptor corepressor 1 pseudogene 1																		TTTTGAAGGTGAAGCATTTTG	0.393																																																	0																																												0			AL391119		20p11.1	2011-09-16	2011-09-16	2011-09-16	ENSG00000240108	ENSG00000240108			16724	pseudogene	pseudogene			"""chromosome 20 open reading frame 191"""	C20orf191			Standard	NR_003678		Approved	bB329D4.2	uc002wvj.5	Q9H4R4	OTTHUMG00000032145		20.37:g.26084228G>A			A2RUA0	RNA	SNP	ENST00000478176.1	37																																																																																					0.393	NCOR1P1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000078478.2			
NCOR1P1	149934	hgsc.bcm.edu	37	20	26084261	26084261	+	RNA	SNP	A	A	G	rs61752354|rs61751718	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr20:26084261A>G	ENST00000478176.1	-	0	196					NR_003678.1		Q9H4R4	CT191_HUMAN	nuclear receptor corepressor 1 pseudogene 1																		CGGTTGCCCCAGAATTGGAGA	0.388																																																	0													32.0	24.0	26.0					20																	26084261		691	1590	2281			0			AL391119		20p11.1	2011-09-16	2011-09-16	2011-09-16	ENSG00000240108	ENSG00000240108			16724	pseudogene	pseudogene			"""chromosome 20 open reading frame 191"""	C20orf191			Standard	NR_003678		Approved	bB329D4.2	uc002wvj.5	Q9H4R4	OTTHUMG00000032145		20.37:g.26084261A>G			A2RUA0	RNA	SNP	ENST00000478176.1	37																																																																																					0.388	NCOR1P1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000078478.2			
DLGAP5	9787	hgsc.bcm.edu;ucsc.edu	37	14	55625420	55625420	+	Missense_Mutation	SNP	C	C	A			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr14:55625420C>A	ENST00000247191.2	-	14	1909	c.1693G>T	c.(1693-1695)Gat>Tat	p.D565Y	DLGAP5_ENST00000395425.2_Missense_Mutation_p.D565Y	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	565					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						CCAGCATCATCCTGTTTTGGT	0.393																																																	0													105.0	97.0	100.0					14																	55625420		2202	4300	6502	SO:0001583	missense	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1693G>T	14.37:g.55625420C>A	ENSP00000247191:p.Asp565Tyr		A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.259919	0.39995	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.17054	2.3;2.3	4.97	4.08	0.47627	.	1.157320	0.06430	N	0.724005	T	0.43456	0.1248	M	0.76002	2.32	0.21220	N	0.999754	D;D	0.64830	0.994;0.994	D;D	0.67103	0.949;0.925	T	0.24225	-1.0166	10	0.62326	D	0.03	.	12.2323	0.54495	0.0:0.9145:0.0:0.0855	.	565;565	A8MTM6;Q15398	.;DLGP5_HUMAN	Y	565	ENSP00000378815:D565Y;ENSP00000247191:D565Y	ENSP00000247191:D565Y	D	-	1	0	DLGAP5	54695173	0.013000	0.17824	0.523000	0.27875	0.351000	0.29236	0.917000	0.28665	2.703000	0.92315	0.655000	0.94253	GAT		0.393	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2		NM_014750	
DPCR1	135656	hgsc.bcm.edu	37	6	30917388	30917388	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs538677376	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr6:30917388C>A	ENST00000304311.2	+	0	1147				DPCR1_ENST00000462446.1_Missense_Mutation_p.H383N|HCG21_ENST00000419481.1_RNA	NM_080870.3	NP_543146.2	Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GCCTACAGAACATGGAGAAAG	0.493													-|||	9	0.00179712	0.0015	0.0	5008	,	,		25455	0.004		0.002	False		,,,				2504	0.001																0													161.0	142.0	147.0					6																	30917388		692	1591	2283			135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000304311.2:c.-2328C>A	6.37:g.30917388C>A			C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000304311.2	37		.	.	.	.	.	.	.	.	.	.	-	2.807	-0.247784	0.05867	.	.	ENSG00000168631	ENST00000462446	T	0.59772	0.24	2.02	1.13	0.20643	.	.	.	.	.	T	0.26593	0.0650	L	0.39245	1.2	0.18873	N	0.999988	P	0.44344	0.833	P	0.44477	0.451	T	0.09292	-1.0681	9	0.17832	T	0.49	.	6.6264	0.22833	0.0:0.8379:0.0:0.1621	.	383	E9PEI6	.	N	383	ENSP00000417182:H383N	ENSP00000417182:H383N	H	+	1	0	DPCR1	31025367	0.000000	0.05858	0.002000	0.10522	0.163000	0.22366	-0.895000	0.04118	0.432000	0.26286	0.430000	0.28490	CAT		0.493	DPCR1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_080870	
EMR2	30817	hgsc.bcm.edu;ucsc.edu	37	19	14877799	14877799	+	Missense_Mutation	SNP	G	G	C	rs12976472	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr19:14877799G>C	ENST00000315576.3	-	6	929	c.478C>G	c.(478-480)Ctc>Gtc	p.L160V	EMR2_ENST00000392967.2_Missense_Mutation_p.L160V|EMR2_ENST00000599423.1_5'Flank|EMR2_ENST00000353005.1_Intron|EMR2_ENST00000601345.1_Missense_Mutation_p.L160V|EMR2_ENST00000596991.2_Missense_Mutation_p.L160V|EMR2_ENST00000594294.1_Missense_Mutation_p.L160V|EMR2_ENST00000392965.3_Missense_Mutation_p.L160V|EMR2_ENST00000594076.1_Intron|EMR2_ENST00000346057.1_Missense_Mutation_p.L160V|EMR2_ENST00000353876.1_Intron|EMR2_ENST00000392964.3_5'UTR|EMR2_ENST00000595839.1_Intron	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	160	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CCTGTGCAGAGCTTCGGGTCC	0.617																																																	0								G	VAL/LEU,VAL/LEU,,,VAL/LEU,VAL/LEU,	1741,2609		740,261,1174	36.0	42.0	40.0		478,478,,,478,478,	-1.3	0.0	19	dbSNP_121	40	2362,6160		964,434,2863	yes	missense,missense,intron,intron,missense,missense,intron	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	32,32,,,32,32,	1704,695,4037	CC,CG,GG		27.7165,40.023,31.8754	benign,benign,,,benign,benign,	160/824,160/775,,,160/813,160/764,	14877799	4103,8769	2175	4261	6436	SO:0001583	missense	30817			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.478C>G	19.37:g.14877799G>C	ENSP00000319883:p.Leu160Val		B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	839	0.3841575091575092	243	0.49390243902439024	152	0.4198895027624309	169	0.29545454545454547	275	0.3627968337730871	G	0.563	-0.844360	0.02671	0.40023	0.277165	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000360222;ENST00000392965;ENST00000392962	T;T;T;T;T	0.78364	-0.86;-0.99;-1.17;-1.15;-1.04	3.06	-1.28	0.09318	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;B;B;B	0.42757	0.789;0.008;0.097;0.019	B;B;B;B	0.40940	0.344;0.019;0.046;0.015	T	0.30297	-0.9983	8	0.09590	T	0.72	.	4.8562	0.13561	0.0:0.2107:0.3614:0.4279	rs12976472	160;160;160;160	E7ESD7;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;EMR2_HUMAN;.	V	160	ENSP00000319883:L160V;ENSP00000376694:L160V;ENSP00000263380:L160V;ENSP00000376692:L160V;ENSP00000376689:L160V	ENSP00000319883:L160V	L	-	1	0	EMR2	14738799	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.286000	0.08399	0.069000	0.16605	0.508000	0.49915	CTC		0.617	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			
GPC6	10082	hgsc.bcm.edu;ucsc.edu	37	13	95034756	95034756	+	Missense_Mutation	SNP	C	C	G			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr13:95034756C>G	ENST00000377047.4	+	7	1856	c.1241C>G	c.(1240-1242)gCg>gGg	p.A414G		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	414					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				AGCGTGACAGCGGGCACGTCC	0.527																																																	0													149.0	133.0	139.0					13																	95034756		2203	4300	6503	SO:0001583	missense	10082			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1241C>G	13.37:g.95034756C>G	ENSP00000366246:p.Ala414Gly		A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.954319	0.53293	.	.	ENSG00000183098	ENST00000377047	T	0.52526	0.66	5.74	5.74	0.90152	.	0.234527	0.42682	D	0.000678	T	0.50429	0.1615	M	0.61703	1.905	0.43195	D	0.99503	B	0.12630	0.006	B	0.24701	0.055	T	0.41070	-0.9529	10	0.36615	T	0.2	.	18.0853	0.89455	0.0:1.0:0.0:0.0	.	414	Q9Y625	GPC6_HUMAN	G	414	ENSP00000366246:A414G	ENSP00000366246:A414G	A	+	2	0	GPC6	93832757	1.000000	0.71417	0.843000	0.33291	0.550000	0.35303	6.307000	0.72815	2.708000	0.92522	0.650000	0.86243	GCG		0.527	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4		NM_005708	
SLC52A2	79581	hgsc.bcm.edu	37	8	145584534	145584535	+	Frame_Shift_Ins	INS	-	-	G	rs144821688		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr8:145584534_145584535insG	ENST00000532887.1	+	5	1780_1781	c.1197_1198insG	c.(1198-1200)gggfs	p.G400fs	FBXL6_ENST00000455319.2_5'Flank|SLC52A2_ENST00000540505.1_Frame_Shift_Ins_p.G312fs|SLC52A2_ENST00000527078.1_Frame_Shift_Ins_p.G400fs|SLC52A2_ENST00000402965.1_Frame_Shift_Ins_p.G400fs|SLC52A2_ENST00000530047.1_Frame_Shift_Ins_p.G400fs|SLC52A2_ENST00000329994.2_Frame_Shift_Ins_p.G400fs|FBXL6_ENST00000331890.5_5'Flank|SLC52A2_ENST00000526752.1_Frame_Shift_Ins_p.R68fs			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	400					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	TGCTGCATGGCGGGGGCCGGCC	0.653																																																	0																																										SO:0001589	frameshift_variant	0			AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"""Solute carriers"""	30224	protein-coding gene	gene with protein product		607882	"""G protein-coupled receptor 172A"""	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.1202dupG	8.37:g.145584539_145584539dupG	ENSP00000436768:p.Gly400fs		A8K6B6|D3DWL8|G1UCY1|Q86UT1	Frame_Shift_Ins	INS	ENST00000532887.1	37	CCDS6423.1																																																																																				0.653	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1		NM_024531	
GPR50	9248	hgsc.bcm.edu;ucsc.edu	37	X	150349558	150349569	+	In_Frame_Del	DEL	CACCACTGGCCA	CACCACTGGCCA	-	rs377556761|rs199797606|rs68058591|rs200787393		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	CACCACTGGCCA	CACCACTGGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chrX:150349558_150349569delCACCACTGGCCA	ENST00000218316.3	+	2	1572_1583	c.1503_1514delCACCACTGGCCA	c.(1501-1515)cccaccactggccac>ccc	p.TTGH502del	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	502	Pro-rich.		Missing (lower fasting circulating triglyceride levels). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)	p.T502_H505delTTGH(1)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					ACCCTAAACCCACCACTGGCCACATCAAGCCA	0.608																																																	1	Deletion - In frame(1)	ovary(1)								1488,2015		315,617,241,554,290						2.6	0.0		dbSNP_130	100	2487,3842		404,1011,668,899,1033	no	coding	GPR50	NM_004224.3		719,1628,909,1453,1323	A1A1,A1R,A1,RR,R		39.2953,42.4779,40.4292				3975,5857				SO:0001651	inframe_deletion	9248			U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1503_1514delCACCACTGGCCA	X.37:g.150349558_150349569delCACCACTGGCCA	ENSP00000218316:p.Thr502_His505del		Q0VGG3|Q3ZAR0	In_Frame_Del	DEL	ENST00000218316.3	37	CCDS44012.1																																																																																				0.608	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1		NM_004224	
HARBI1	283254	hgsc.bcm.edu;ucsc.edu	37	11	46625224	46625224	+	Silent	SNP	G	G	A			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr11:46625224G>A	ENST00000326737.3	-	3	1153	c.906C>T	c.(904-906)tcC>tcT	p.S302S		NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	302						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclease activity (GO:0004518)			large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	3						CATGCTCCAGGGAGATGTTGT	0.557																																																	0													87.0	79.0	82.0					11																	46625224		2201	4299	6500	SO:0001819	synonymous_variant	283254			AK057237	CCDS7920.1	11p11.2	2008-07-10	2008-07-01	2008-07-01	ENSG00000180423	ENSG00000180423			26522	protein-coding gene	gene with protein product		615086	"""chromosome 11 open reading frame 77"""	C11orf77		15169610, 18339812	Standard	NM_173811		Approved	FLJ32675	uc001ncy.3	Q96MB7	OTTHUMG00000166537	ENST00000326737.3:c.906C>T	11.37:g.46625224G>A			D3DQP9	Silent	SNP	ENST00000326737.3	37	CCDS7920.1																																																																																				0.557	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1		NM_173811	
HMCN1	83872	hgsc.bcm.edu;ucsc.edu	37	1	185939611	185939611	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:185939611delC	ENST00000271588.4	+	15	2586	c.2357delC	c.(2356-2358)actfs	p.T786fs	HMCN1_ENST00000485744.1_3'UTR|HMCN1_ENST00000367492.2_Frame_Shift_Del_p.T786fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	786	Ig-like C2-type 4.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGCAAGATAACTCTGGATGTT	0.388																																																	0													123.0	124.0	124.0					1																	185939611		2203	4300	6503	SO:0001589	frameshift_variant	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.2357delC	1.37:g.185939611delC	ENSP00000271588:p.Thr786fs		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Del	DEL	ENST00000271588.4	37	CCDS30956.1																																																																																				0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1		NM_031935	
IBSP	3381	hgsc.bcm.edu;ucsc.edu	37	4	88732929	88732929	+	Missense_Mutation	SNP	G	G	C			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr4:88732929G>C	ENST00000226284.5	+	7	888	c.821G>C	c.(820-822)gGa>gCa	p.G274A		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	274					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		TACGACAATGGATATGAAATC	0.478																																																	0													66.0	63.0	64.0					4																	88732929		2203	4300	6503	SO:0001583	missense	3381				CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.821G>C	4.37:g.88732929G>C	ENSP00000226284:p.Gly274Ala			Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693487	0.30052	.	.	ENSG00000029559	ENST00000226284	T	0.11930	2.73	5.36	-0.849	0.10723	.	0.507607	0.19563	N	0.111283	T	0.11024	0.0269	L	0.48362	1.52	0.09310	N	1	B	0.20887	0.049	B	0.26693	0.072	T	0.24083	-1.0170	10	0.38643	T	0.18	.	6.3411	0.21322	0.214:0.3753:0.4107:0.0	.	274	P21815	SIAL_HUMAN	A	274	ENSP00000226284:G274A	ENSP00000226284:G274A	G	+	2	0	IBSP	88951953	0.646000	0.27295	0.029000	0.17559	0.985000	0.73830	1.021000	0.30040	-0.586000	0.05898	0.591000	0.81541	GGA		0.478	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2			
IGFN1	91156	hgsc.bcm.edu	37	1	201180222	201180222	+	Silent	SNP	G	G	A	rs28465285		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:201180222G>A	ENST00000335211.4	+	12	6331	c.6201G>A	c.(6199-6201)gaG>gaA	p.E2067E	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	924						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAGTGAATGAGGCAGGTTATA	0.473																																																	0													30.0	25.0	26.0					1																	201180222		692	1591	2283	SO:0001819	synonymous_variant	91156			AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.6201G>A	1.37:g.201180222G>A			F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																				0.473	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_178275	
IGFN1	91156	hgsc.bcm.edu	37	1	201180243	201180243	+	Silent	SNP	A	A	G	rs367952435		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:201180243A>G	ENST00000335211.4	+	12	6352	c.6222A>G	c.(6220-6222)ttA>ttG	p.L2074L	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	0						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GGAAGGATTTAGGGGCTCCTA	0.468																																																	0													32.0	27.0	29.0					1																	201180243		692	1591	2283	SO:0001819	synonymous_variant	91156			AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.6222A>G	1.37:g.201180243A>G			F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																				0.468	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_178275	
IMPG2	50939	hgsc.bcm.edu;ucsc.edu	37	3	101023037	101023037	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr3:101023037C>T	ENST00000193391.7	-	3	641	c.454G>A	c.(454-456)Ggc>Agc	p.G152S		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	152					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	AAATTTGTGCCCATTTCAAAT	0.408																																																	0													159.0	154.0	156.0					3																	101023037		2203	4300	6503	SO:0001583	missense	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.454G>A	3.37:g.101023037C>T	ENSP00000193391:p.Gly152Ser		A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	35	5.473714	0.96291	.	.	ENSG00000081148	ENST00000193391	T	0.52526	0.66	5.75	5.75	0.90469	.	0.153092	0.45126	D	0.000388	T	0.67154	0.2863	M	0.75615	2.305	0.54753	D	0.999987	D;D	0.64830	0.994;0.989	P;P	0.58331	0.837;0.68	T	0.69587	-0.5105	10	0.72032	D	0.01	-2.7229	19.5356	0.95253	0.0:1.0:0.0:0.0	.	152;152	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	S	152	ENSP00000193391:G152S	ENSP00000193391:G152S	G	-	1	0	IMPG2	102505727	1.000000	0.71417	0.990000	0.47175	0.988000	0.76386	7.380000	0.79704	2.716000	0.92895	0.650000	0.86243	GGC		0.408	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			
IQGAP1	8826	hgsc.bcm.edu;ucsc.edu	37	15	91021009	91021010	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr15:91021009_91021010GC>TA	ENST00000268182.5	+	26	3341_3342	c.3217_3218GC>TA	c.(3217-3219)GCc>TAc	p.A1073Y	IQGAP1_ENST00000560738.1_Missense_Mutation_p.A501Y	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1073	C1.|Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ACAGATCTTGGCCCCAGTCGTG	0.431																																																	0																																										SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	Exception_encountered	15.37:g.91021009_91021010delinsTA	ENSP00000268182:p.Ala1073Tyr		A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1																																																																																				0.431	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1		NM_003870	
KCTD19	146212	hgsc.bcm.edu;ucsc.edu	37	16	67327544	67327545	+	In_Frame_Ins	INS	-	-	GCTCCA	rs372339467|rs567420800|rs143567769	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr16:67327544_67327545insGCTCCA	ENST00000304372.5	-	12	2175_2176	c.2120_2121insTGGAGC	c.(2119-2121)gcg>gcTGGAGCg	p.707_707A>AGA		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	707					protein homooligomerization (GO:0051260)			p.A707A(1)		endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		CCTTGTCTTTCGCTCCAGCTCC	0.599														4	0.000798722	0.0	0.0014	5008	,	,		16372	0.0		0.003	False		,,,				2504	0.0																1	Substitution - coding silent(1)	skin(1)								1,3773		0,1,1886						0.1	0.0			93	21,7907		1,19,3944	no	coding	KCTD19	NM_001100915.1		1,20,5830	A1A1,A1R,RR		0.2649,0.0265,0.188				22,11680				SO:0001652	inframe_insertion	146212			AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2115_2120dupTGGAGC	16.37:g.67327545_67327550dupGCTCCA	ENSP00000305702:p.GlyAla707dup		B4DZ49|Q8N804	In_Frame_Ins	INS	ENST00000304372.5	37	CCDS42179.1																																																																																				0.599	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1		XM_085367	
KIAA0020	9933	hgsc.bcm.edu;ucsc.edu	37	9	2807851	2807851	+	Missense_Mutation	SNP	A	A	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr9:2807851A>T	ENST00000397885.2	-	17	1983	c.1777T>A	c.(1777-1779)Tgg>Agg	p.W593R		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	593						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		ACACTAGCCCAGGACTTCAGG	0.393																																																	0													124.0	109.0	114.0					9																	2807851		2203	4300	6503	SO:0001583	missense	9933			AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1777T>A	9.37:g.2807851A>T	ENSP00000380982:p.Trp593Arg		A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	A	17.59	3.428230	0.62844	.	.	ENSG00000080608	ENST00000397885	T	0.13538	2.58	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (1);	0.104913	0.64402	D	0.000001	T	0.42337	0.1198	M	0.84948	2.725	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.45131	-0.9282	10	0.87932	D	0	-16.7665	14.9163	0.70801	1.0:0.0:0.0:0.0	.	453;593	B2RDG4;Q15397	.;K0020_HUMAN	R	593	ENSP00000380982:W593R	ENSP00000380982:W593R	W	-	1	0	KIAA0020	2797851	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	7.097000	0.76967	2.261000	0.74972	0.533000	0.62120	TGG		0.393	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3		NM_014878	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31913982	31913982	+	Frame_Shift_Del	DEL	G	G	-	rs5843453|rs201420116|rs570064399	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr21:31913982delG	ENST00000334046.5	-	1	201	c.171delC	c.(169-171)ttcfs	p.F57fs		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	57						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTTTTTAGTAGAATCCAGAGA	0.463													?|G|-|unsure	3942	0.787141	0.9266	0.7421	5008	,	,		17489	0.7034		0.7127	False		,,,				2504	0.7935																0													33.0	58.0	51.0					21																	31913982		1069	2843	3912	SO:0001589	frameshift_variant	337973			AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.171delC	21.37:g.31913982delG	ENSP00000375107:p.Phe57fs		Q3LI71	Frame_Shift_Del	DEL	ENST00000334046.5	37	CCDS13598.1																																																																																				0.463	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4			
MUC4	4585	hgsc.bcm.edu	37	3	195515449	195515449	+	Missense_Mutation	SNP	A	A	T	rs200672669	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr3:195515449A>T	ENST00000463781.3	-	2	3461	c.3002T>A	c.(3001-3003)gTa>gAa	p.V1001E	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V1001E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	425	Ser-rich.				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.V1001A(1)|p.V1001E(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)		ACCTGTGGATACTGAGGAAGC	0.587																																																	2	Substitution - Missense(2)	prostate(1)|endometrium(1)											45.0	36.0	39.0					3																	195515449		2193	4257	6450	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.3002T>A	3.37:g.195515449A>T	ENSP00000417498:p.Val1001Glu		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	.	.	.	.	.	.	.	.	.	.	A	7.806	0.714656	0.15306	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.19;1.18	1.24	-2.48	0.06423	.	.	.	.	.	T	0.13543	0.0328	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.01281	0.0	T	0.24261	-1.0165	8	.	.	.	.	2.7997	0.05411	0.2821:0.0:0.4902:0.2277	.	1001	E7ESK3	.	E	1001	ENSP00000417498:V1001E;ENSP00000420243:V1001E	.	V	-	2	0	MUC4	196999844	.	.	0.000000	0.03702	0.127000	0.20565	.	.	-0.712000	0.04988	0.055000	0.15244	GTA		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
OR1L4	254973	hgsc.bcm.edu	37	9	125486717	125486717	+	Missense_Mutation	SNP	G	G	A	rs76170289		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr9:125486717G>A	ENST00000259466.1	+	1	449	c.449G>A	c.(448-450)tGc>tAc	p.C150Y		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						TTGGGTTCTTGCAGCATCTCC	0.502																																																	0													230.0	184.0	199.0					9																	125486717		2203	4300	6503	SO:0001583	missense	254973				CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"""GPCR / Class A : Olfactory receptors"""	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.449G>A	9.37:g.125486717G>A	ENSP00000259466:p.Cys150Tyr		Q6IFN0|Q96R81	Missense_Mutation	SNP	ENST00000259466.1	37	CCDS35129.1	.	.	.	.	.	.	.	.	.	.	.	13.85	2.359846	0.41801	.	.	ENSG00000136939	ENST00000259466	T	0.35605	1.3	4.01	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.102403	0.44483	D	0.000453	T	0.26521	0.0648	N	0.01146	-0.985	0.37012	D	0.89577	D	0.89917	1.0	D	0.91635	0.999	T	0.43621	-0.9380	10	0.72032	D	0.01	-25.1842	7.3285	0.26569	0.0988:0.1739:0.7273:0.0	.	150	Q8NGR5	OR1L4_HUMAN	Y	150	ENSP00000259466:C150Y	ENSP00000259466:C150Y	C	+	2	0	OR1L4	124526538	0.027000	0.19231	1.000000	0.80357	0.767000	0.43475	0.314000	0.19432	2.079000	0.62486	0.298000	0.19748	TGC		0.502	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1			
OR2T4	127074	hgsc.bcm.edu	37	1	248525308	248525308	+	Silent	SNP	A	A	G	rs201411128		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:248525308A>G	ENST00000366475.1	+	1	426	c.426A>G	c.(424-426)tcA>tcG	p.S142S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TAGCAGGTTCAGAATTTTTCC	0.527																																																	0																																										SO:0001819	synonymous_variant	127074			BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.426A>G	1.37:g.248525308A>G			Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																				0.527	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2		NM_001004696	
OR4C3	256144	hgsc.bcm.edu;ucsc.edu	37	11	48346661	48346669	+	In_Frame_Del	DEL	TTGCTGATC	TTGCTGATC	-	rs201980031|rs138704181		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	TTGCTGATC	TTGCTGATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr11:48346661_48346669delTTGCTGATC	ENST00000319856.4	+	1	190_198	c.169_177delTTGCTGATC	c.(169-177)ttgctgatcdel	p.LLI57del		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TGTGGTCTTTTTGCTGATCTATGTGGTCA	0.469																																																	0										1956,2308		0,1956,176						-1.1	0.0		dbSNP_126	130	3671,4583		0,3671,456	no	coding	OR4C3	NM_001004702.1		0,5627,632	A1A1,A1R,RR		44.4754,45.8724,44.9513				5627,6891				SO:0001651	inframe_deletion	256144			AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"""GPCR / Class A : Olfactory receptors"""	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.169_177delTTGCTGATC	11.37:g.48346661_48346669delTTGCTGATC	ENSP00000321419:p.Leu57_Ile59del		B2RNF2|Q6IFB3	In_Frame_Del	DEL	ENST00000319856.4	37	CCDS31489.1																																																																																				0.469	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1		NM_001004702	
OR52J3	119679	hgsc.bcm.edu	37	11	5068656	5068656	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr11:5068656C>T	ENST00000380370.1	+	1	901	c.901C>T	c.(901-903)Cga>Tga	p.R301*		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAACAGATTCGAGAACGAGT	0.383																																																	0													65.0	61.0	62.0					11																	5068656		2201	4298	6499	SO:0001587	stop_gained	119679			AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.901C>T	11.37:g.5068656C>T	ENSP00000369728:p.Arg301*		Q6IFE4	Nonsense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.391653	0.25118	.	.	ENSG00000205495	ENST00000380370	.	.	.	4.19	-6.69	0.01772	.	0.164651	0.27262	N	0.020168	.	.	.	.	.	.	0.31000	N	0.720457	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2663	0.31815	0.6404:0.1399:0.0:0.2197	.	.	.	.	X	301	.	ENSP00000369728:R301X	R	+	1	2	OR52J3	5025232	0.000000	0.05858	0.033000	0.17914	0.001000	0.01503	-3.100000	0.00604	-1.316000	0.02295	-0.989000	0.02550	CGA		0.383	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1		NM_001001916	
OR4C4P	79550	hgsc.bcm.edu	37	11	48373827	48373827	+	IGR	SNP	G	G	A	rs80081241	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr11:48373827G>A								OR4C3 (26320 upstream) : OR4C5 (13209 downstream)																							CAAATAGGACGGAAAAGAGTA	0.413													N|||	117	0.0233626	0.0847	0.0072	5008	,	,		12643	0.0		0.0	False		,,,				2504	0.0																0													131.0	111.0	117.0					11																	48373827		692	1591	2283	SO:0001628	intergenic_variant	403257																															11.37:g.48373827G>A				Missense_Mutation	SNP		37																																																																																				0	0.413									
AKAP2	11217	hgsc.bcm.edu;ucsc.edu	37	9	112900341	112900342	+	In_Frame_Ins	INS	-	-	GAAGCT	rs373159646|rs34665027|rs150402481	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr9:112900341_112900342insGAAGCT	ENST00000259318.7	+	2	2031_2032	c.1824_1825insGAAGCT	c.(1825-1827)gaa>GAAGCTgaa	p.609_609E>EAE	PALM2-AKAP2_ENST00000374530.3_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000555236.1_In_Frame_Ins_p.840_840E>EAE|PALM2-AKAP2_ENST00000302798.7_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000510514.5_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000434623.2_In_Frame_Ins_p.698_698E>EAE|AKAP2_ENST00000374525.1_In_Frame_Ins_p.698_698E>EAE	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	609								p.E839_E840insEA(1)|p.E697_E698insEA(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CGACTGTAGAGGAAGCTGAAGC	0.505														656	0.13099	0.1309	0.0821	5008	,	,		20174	0.2133		0.1362	False		,,,				2504	0.0757																2	Insertion - In frame(2)	lung(2)							,,,,	550,3714		39,472,1621					,,,,	2.7	0.9		dbSNP_134	39	1146,7108		82,982,3063	no	coding,coding,coding,coding,coding	AKAP2,PALM2-AKAP2	NM_147150.2,NM_007203.4,NM_001198656.1,NM_001136562.2,NM_001004065.4	,,,,	121,1454,4684	A1A1,A1R,RR		13.8842,12.8987,13.5485	,,,,	,,,,		1696,10822				SO:0001652	inframe_insertion	445815			AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1831_1836dupGAAGCT	9.37:g.112900342_112900347dupGAAGCT	Exception_encountered		B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	In_Frame_Ins	INS	ENST00000259318.7	37	CCDS48003.1																																																																																				0.505	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3		NM_001004065	
PCNT	5116	hgsc.bcm.edu	37	21	47754449	47754449	+	Missense_Mutation	SNP	G	G	A	rs59183158		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr21:47754449G>A	ENST00000359568.5	+	3	513	c.406G>A	c.(406-408)Ggt>Agt	p.G136S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	136					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GTTCACAGTCGGTGACCACCC	0.552																																																	0													180.0	121.0	141.0					21																	47754449		2203	4300	6503	SO:0001583	missense	5116			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.406G>A	21.37:g.47754449G>A	ENSP00000352572:p.Gly136Ser		O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	a	0.003	-2.400549	0.00195	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	0.158	-0.317	0.12736	.	.	.	.	.	T	0.00637	0.0021	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49969	-0.8882	8	0.41790	T	0.15	.	.	.	.	rs59183158	18;136	O95613-2;O95613	.;PCNT_HUMAN	S	136	ENSP00000352572:G136S	ENSP00000338675:G136S	G	+	1	0	PCNT	46578877	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.839000	0.00738	-2.864000	0.00326	-2.902000	0.00092	GGT		0.552	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1		NM_006031	
POLR1E	64425	hgsc.bcm.edu;ucsc.edu	37	9	37495950	37495950	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr9:37495950C>T	ENST00000377798.4	+	8	832	c.719C>T	c.(718-720)tCa>tTa	p.S240L	POLR1E_ENST00000442009.2_Missense_Mutation_p.S170L|POLR1E_ENST00000377792.3_Missense_Mutation_p.S302L	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	293					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		AACGTCACGTCAGAAGAAATA	0.463																																					Ovarian(116;843 1620 18506 32459 34463)												0													123.0	116.0	118.0					9																	37495950		2203	4300	6503	SO:0001583	missense	64425			AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.719C>T	9.37:g.37495950C>T	ENSP00000367029:p.Ser240Leu		O75395|Q5JTE3	Missense_Mutation	SNP	ENST00000377798.4	37	CCDS6611.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513413	0.85389	.	.	ENSG00000137054	ENST00000377798;ENST00000442009;ENST00000377792	T;T;T	0.23552	1.9;1.9;1.9	5.38	5.38	0.77491	.	0.419598	0.26824	N	0.022313	T	0.41696	0.1170	M	0.64997	1.995	0.42278	D	0.992081	P;D;P	0.54397	0.942;0.966;0.921	P;P;P	0.55749	0.783;0.61;0.52	T	0.05007	-1.0912	10	0.27785	T	0.31	-2.8018	16.6817	0.85294	0.0:1.0:0.0:0.0	.	170;302;240	E7EX70;Q9GZS1;Q9GZS1-2	.;RPA49_HUMAN;.	L	240;170;302	ENSP00000367029:S240L;ENSP00000399887:S170L;ENSP00000367023:S302L	ENSP00000367023:S302L	S	+	2	0	POLR1E	37485950	0.961000	0.32948	0.988000	0.46212	0.983000	0.72400	4.813000	0.62620	2.793000	0.96121	0.655000	0.94253	TCA		0.463	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1		NM_022490	
PHF2	5253	hgsc.bcm.edu;ucsc.edu	37	9	96439004	96439004	+	Silent	SNP	C	C	A	rs75653373|rs149736720|rs368818072	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr9:96439004C>A	ENST00000359246.4	+	21	3328	c.2961C>A	c.(2959-2961)acC>acA	p.T987T	PHF2_ENST00000375376.4_Silent_p.T218T	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	987	Ser/Thr-rich.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.T987_P988insPASTT(1)|p.T987T(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		cctctaccaccccggcctcca	0.692																																																	2	Insertion - In frame(1)|Substitution - coding silent(1)	large_intestine(1)|central_nervous_system(1)											82.0	60.0	68.0					9																	96439004		2155	4247	6402	SO:0001819	synonymous_variant	5253			AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2961C>A	9.37:g.96439004C>A			Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																				0.692	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1		NM_005392	
PPAP2C	8612	hgsc.bcm.edu;ucsc.edu	37	19	282291	282291	+	Missense_Mutation	SNP	A	A	G			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr19:282291A>G	ENST00000269812.3	-	5	609	c.560T>C	c.(559-561)cTc>cCc	p.L187P	PPAP2C_ENST00000327790.3_Missense_Mutation_p.L208P|PPAP2C_ENST00000434325.2_Missense_Mutation_p.L131P	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	187					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCCAACAGAGTCGTGCCTG	0.612																																																	0													82.0	68.0	73.0					19																	282291		2203	4300	6503	SO:0001583	missense	8612			AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.560T>C	19.37:g.282291A>G	ENSP00000269812:p.Leu187Pro		A6NLV0|E9PAY8	Missense_Mutation	SNP	ENST00000269812.3	37	CCDS12023.1	.	.	.	.	.	.	.	.	.	.	.	17.88	3.498205	0.64186	.	.	ENSG00000141934	ENST00000269812;ENST00000327790;ENST00000434325	T;T;T	0.41065	1.05;1.01;1.01	4.8	4.8	0.61643	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.081401	0.50627	U	0.000105	T	0.70988	0.3287	M	0.92317	3.295	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.992;0.988	T	0.79047	-0.1963	10	0.87932	D	0	-18.2105	13.2401	0.59992	1.0:0.0:0.0:0.0	.	187;208	O43688;O43688-2	LPP2_HUMAN;.	P	187;208;131	ENSP00000269812:L187P;ENSP00000329697:L208P;ENSP00000388565:L131P	ENSP00000269812:L187P	L	-	2	0	PPAP2C	233291	1.000000	0.71417	0.038000	0.18304	0.673000	0.39480	8.774000	0.91767	1.818000	0.53035	0.369000	0.22263	CTC		0.612	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			
PRB1	5542	hgsc.bcm.edu	37	12	11506654	11506654	+	Intron	SNP	C	C	T	rs199775084		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr12:11506654C>T	ENST00000500254.2	-	3	351				PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACCTTGAGGTCTGTTGCCTCC	0.602																																																	0													17.0	15.0	16.0					12																	11506654		1290	2284	3574	SO:0001627	intron_variant	5542				CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.313+69G>A	12.37:g.11506654C>T			Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1																																																																																				0.602	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1		NM_005039	
PRKCH	5583	hgsc.bcm.edu;ucsc.edu	37	14	62014499	62014499	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr14:62014499delG	ENST00000332981.5	+	13	2185	c.1800delG	c.(1798-1800)ctgfs	p.L600fs	PRKCH_ENST00000555082.1_Frame_Shift_Del_p.L439fs|RP11-47I22.4_ENST00000556347.1_Frame_Shift_Del_p.*105fs|PRKCH_ENST00000556245.1_3'UTR|RP11-47I22.1_ENST00000556543.1_RNA	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		TGGGCAGCCTGACTCAGGGAG	0.507																																					Melanoma(135;863 1779 8064 14443 26348)												0													264.0	265.0	265.0					14																	62014499		2203	4300	6503	SO:0001589	frameshift_variant	5583			M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.1800delG	14.37:g.62014499delG	ENSP00000329127:p.Leu600fs		B4DJN5|Q16246|Q8NE03	Frame_Shift_Del	DEL	ENST00000332981.5	37	CCDS9752.1																																																																																				0.507	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2		NM_006255	
RAB11FIP3	9727	hgsc.bcm.edu;ucsc.edu	37	16	546818	546826	+	Splice_Site	DEL	GCACAGTCC	GCACAGTCC	-	rs201535149|rs267604564		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	GCACAGTCC	GCACAGTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr16:546818_546826delGCACAGTCC	ENST00000262305.4	+	6	1653_1656	c.1265_1268delGCACAGTCC	c.(1264-1269)agcaca>aa	p.ST422del	RAB11FIP3_ENST00000457159.1_Splice_Site_p.ST467del|RAB11FIP3_ENST00000450428.1_Splice_Site_p.ST126del	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	422					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				TTTGTTTTCTGCACAGTCCGACAAAGCGG	0.459																																					Melanoma(160;2366 2595 4474 8099)												0																																										SO:0001630	splice_region_variant	9727			AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1266-1GCACAGTCC>-	16.37:g.546818_546826delGCACAGTCC			B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Frame_Shift_Del	DEL	ENST00000262305.4	37	CCDS32351.1																																																																																				0.459	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4		NM_014700	In_Frame_Del
RAI1	10743	hgsc.bcm.edu	37	17	17700038	17700040	+	In_Frame_Del	DEL	AGG	AGG	-	rs149716029|rs398124417	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr17:17700038_17700040delAGG	ENST00000353383.1	+	3	4245_4247	c.3776_3778delAGG	c.(3775-3780)aaggag>aag	p.E1261del	RAI1_ENST00000261641.6_In_Frame_Del_p.E1261del	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1261					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGAGATGGGAAGGAGGAGAGGCC	0.631														4	0.000798722	0.0	0.0	5008	,	,		17056	0.0		0.004	False		,,,				2504	0.0																0										15,4249		3,9,2120						3.4	0.5		dbSNP_134	39	72,8182		10,52,4065	no	coding	RAI1	NM_030665.3		13,61,6185	A1A1,A1R,RR		0.8723,0.3518,0.695				87,12431				SO:0001651	inframe_deletion	10743			AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.3776_3778delAGG	17.37:g.17700041_17700043delAGG	ENSP00000323074:p.Glu1261del		Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	In_Frame_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																				0.631	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1		NM_030665	
REV1	51455	hgsc.bcm.edu;ucsc.edu	37	2	100019183	100019183	+	Silent	SNP	T	T	G			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr2:100019183T>G	ENST00000258428.3	-	21	3693	c.3465A>C	c.(3463-3465)ccA>ccC	p.P1155P	REV1_ENST00000465835.1_5'Flank|REV1_ENST00000393445.3_Silent_p.P1154P|RP11-527J8.1_ENST00000608144.1_RNA	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1155	Protein interaction domain; mediates interaction with DNA polymerase zeta.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GATTGGGTGCTGGAGGTCTCA	0.468								Direct reversal of damage																																									0													95.0	96.0	96.0					2																	100019183		2203	4300	6503	SO:0001819	synonymous_variant	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3465A>C	2.37:g.100019183T>G			O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	CCDS2045.1																																																																																				0.468	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2		NM_016316	
RIMS2	9699	hgsc.bcm.edu;ucsc.edu	37	8	105025708	105025708	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr8:105025708C>T	ENST00000507740.1	+	16	2761	c.2525C>T	c.(2524-2526)tCc>tTc	p.S842F	RIMS2_ENST00000406091.3_Missense_Mutation_p.S1028F|RIMS2_ENST00000436393.2_Intron|RIMS2_ENST00000262231.10_Missense_Mutation_p.S867F	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1090	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TATCACAGATCCAGATCAACA	0.478										HNSCC(12;0.0054)																																							0													93.0	93.0	93.0					8																	105025708		1977	4157	6134	SO:0001583	missense	9699			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000507740.1:c.2525C>T	8.37:g.105025708C>T	ENSP00000423559:p.Ser842Phe		B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000507740.1	37	CCDS43761.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.702830	0.68501	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894	T;T;T;T;T	0.22134	1.97;2.51;2.23;2.27;2.12	5.58	5.58	0.84498	.	.	.	.	.	T	0.40015	0.1100	L	0.39898	1.24	0.80722	D	1	D;D;D;P	0.71674	0.998;0.991;0.968;0.935	D;D;P;P	0.70487	0.969;0.918;0.805;0.765	T	0.09530	-1.0670	9	0.62326	D	0.03	.	19.19	0.93663	0.0:1.0:0.0:0.0	.	1090;867;842;1028	Q9UQ26;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.	F	1028;1065;1028;1090;867;842;842	ENSP00000427018:S1028F;ENSP00000384892:S1028F;ENSP00000262231:S867F;ENSP00000423559:S842F;ENSP00000386228:S842F	ENSP00000262231:S867F	S	+	2	0	RIMS2	105094884	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.636000	0.67848	2.636000	0.89361	0.460000	0.39030	TCC		0.478	RIMS2-005	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367215.1		NM_001100117	
RNPC3	55599	hgsc.bcm.edu;ucsc.edu	37	1	104070330	104070330	+	Missense_Mutation	SNP	T	T	C			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:104070330T>C	ENST00000533099.1	+	3	442	c.206T>C	c.(205-207)tTt>tCt	p.F69S	RNPC3_ENST00000423855.2_Missense_Mutation_p.F69S|RNPC3_ENST00000524631.1_Missense_Mutation_p.F69S|RP11-153F1.1_ENST00000444810.1_RNA|RP11-153F1.1_ENST00000447322.2_RNA			Q96LT9	RBM40_HUMAN	RNA-binding region (RNP1, RRM) containing 3	69	Necessary for interaction with PDCD7.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Lung(183;0.111)|Epithelial(280;0.122)|all cancers(265;0.125)|Colorectal(144;0.163)		CATACAGCTTTTGCCACATTC	0.333																																																	0													144.0	119.0	127.0					1																	104070330		692	1590	2282	SO:0001583	missense	55599			AB058742, AY099329	CCDS781.1	1p21.1	2013-07-16			ENSG00000185946	ENSG00000185946		"""RNA binding motif (RRM) containing"""	18666	protein-coding gene	gene with protein product	"""U11/U12 snRNP 65K"""					14974681, 15146077	Standard	NM_017619		Approved	KIAA1839, FLJ20008, RBM40, SNRNP65	uc010oun.2	Q96LT9	OTTHUMG00000166613	ENST00000533099.1:c.206T>C	1.37:g.104070330T>C	ENSP00000432886:p.Phe69Ser		A8K1C9|D3DT74|Q5TZ87|Q96FK7|Q96JI8|Q9NSU7|Q9NXX2	Missense_Mutation	SNP	ENST00000533099.1	37	CCDS781.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296311	0.81025	.	.	ENSG00000185946	ENST00000524631;ENST00000531883;ENST00000533099;ENST00000423855	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.4	5.4	0.78164	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	H	0.98525	4.255	0.58432	D	0.999993	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	T	0.81607	-0.0856	10	0.87932	D	0	-20.2454	15.3799	0.74648	0.0:0.0:0.0:1.0	.	69;69	A8K1C9;Q96LT9	.;RBM40_HUMAN	S	69	ENSP00000437278:F69S;ENSP00000431344:F69S;ENSP00000432886:F69S;ENSP00000391432:F69S	ENSP00000391432:F69S	F	+	2	0	RNPC3	103842918	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.846000	0.69444	2.172000	0.68678	0.460000	0.39030	TTT		0.333	RNPC3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390812.1		NM_017619	
SAG	6295	hgsc.bcm.edu	37	2	234240287	234240287	+	Splice_Site	SNP	G	G	A			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr2:234240287G>A	ENST00000409110.1	+	10	965	c.735G>A	c.(733-735)gtG>gtA	p.V245V	SAG_ENST00000449594.2_Splice_Site_p.V111V	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	245					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CCCTTGCAGTGGAACAGGTGG	0.582																																																	0													110.0	113.0	112.0					2																	234240287		2049	4192	6241	SO:0001630	splice_region_variant	6295				CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.734-1G>A	2.37:g.234240287G>A			A0FDN6|Q53SV3|Q99858	Silent	SNP	ENST00000409110.1	37	CCDS46545.1																																																																																				0.582	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1		NM_000541	Silent
SRGAP2	23380	hgsc.bcm.edu	37	1	206566903	206566903	+	Splice_Site	SNP	G	G	A	rs2987927	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr1:206566903G>A	ENST00000414007.1	+	3	284	c.284G>A	c.(283-285)cGt>cAt	p.R95H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	235	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CCTTTTCAGCGTCAAGCCAAG	0.408													g|||	3	0.000599042	0.0	0.0014	5008	,	,		35930	0.0		0.002	False		,,,				2504	0.0																0													78.0	67.0	70.0					1																	206566903		1899	4122	6021	SO:0001630	splice_region_variant	23380			AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.283-1G>A	1.37:g.206566903G>A				Silent	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	g	32	5.192443	0.94960	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.55930	0.49	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.75925	0.3916	.	.	.	0.80722	D	1.000000	D;D;D	0.89917	1.0;0.996;0.958	D;P;B	0.83275	0.996;0.728;0.425	T	0.78645	-0.2123	8	0.87932	D	0	.	19.5856	0.95488	0.0:0.0:1.0:0.0	rs2987927;rs4844666	82;235;235	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	149;95	ENSP00000390898:R95H	ENSP00000390898:R95H	R	+	2	0	SRGAP2	204633526	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.864000	0.99589	2.625000	0.88918	0.555000	0.69702	CGT		0.408	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding			NM_015326	Missense_Mutation
TATDN1	83940	hgsc.bcm.edu;ucsc.edu	37	8	125527986	125527986	+	Splice_Site	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr8:125527986C>T	ENST00000276692.6	-	6	427		c.e6+1		TATDN1_ENST00000519548.1_Splice_Site|TATDN1_ENST00000521546.1_Splice_Site|TATDN1_ENST00000517678.1_Splice_Site|TATDN1_ENST00000605953.1_Splice_Site	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			AATTTCCTTACTTGAGTTGAG	0.289																																																	0													48.0	49.0	49.0					8																	125527986		2203	4300	6503	SO:0001630	splice_region_variant	83940			AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068	ENST00000276692.6:c.389+1G>A	8.37:g.125527986C>T			B2R5J0|Q8TD02|Q9BY40	Splice_Site	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727040	0.69074	.	.	ENSG00000147687	ENST00000276692;ENST00000519548;ENST00000522810;ENST00000517678;ENST00000519232;ENST00000523888;ENST00000523152	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3125	0.94195	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TATDN1	125597167	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	6.864000	0.75494	2.570000	0.86706	0.563000	0.77884	.		0.289	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1		NM_032026	Intron
TCEAL6	158931	hgsc.bcm.edu	37	X	101395780	101395781	+	Frame_Shift_Ins	INS	-	-	G	rs111588852|rs11408120|rs377261254|rs200987681		TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chrX:101395780_101395781insG	ENST00000372774.3	-	3	772_773	c.523_524insC	c.(523-525)caafs	p.Q175fs	TCEAL6_ENST00000372773.1_Frame_Shift_Ins_p.Q175fs	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						GTTGTCCCCTTGGGCGAATGGA	0.5													GGGG|GGG|GGGG|deletion	3775	1.0	0.7587	0.755	3775	,	,		8751	0.7579		0.7614	False		,,,				2504	0.7342																0										3451,87		1435,63,518,10,4						-5.6	0.0		dbSNP_130	12	6076,139		2190,82,1614,14,29	no	frameshift	TCEAL6	NM_001006938.2		3625,145,2132,24,33	A1A1,A1R,A1,RR,R		2.2365,2.459,2.3172				9527,226				SO:0001589	frameshift_variant	158931			BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.524dupC	X.37:g.101395783_101395783dupG	ENSP00000361860:p.Gln175fs		Q5H9J8	Frame_Shift_Ins	INS	ENST00000372774.3	37	CCDS43978.1																																																																																				0.500	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1		NM_001006938	
TEC	7006	hgsc.bcm.edu;ucsc.edu	37	4	48139497	48139497	+	Missense_Mutation	SNP	G	G	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr4:48139497G>T	ENST00000381501.3	-	18	1989	c.1832C>A	c.(1831-1833)tCt>tAt	p.S611Y		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	611	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						ATCTTCGAAAGAAGGCCTTCC	0.438																																																	0													110.0	103.0	106.0					4																	48139497		2203	4300	6503	SO:0001583	missense	100124696			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1832C>A	4.37:g.48139497G>T	ENSP00000370912:p.Ser611Tyr		B7ZKZ6|Q3MIS5	Missense_Mutation	SNP	ENST00000381501.3	37	CCDS3481.1	.	.	.	.	.	.	.	.	.	.	G	9.125	1.009856	0.19277	.	.	ENSG00000135605	ENST00000381501	T	0.66995	-0.24	4.95	4.95	0.65309	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.176248	0.37136	N	0.002229	T	0.76659	0.4018	M	0.86268	2.805	0.30554	N	0.765128	P	0.44734	0.842	P	0.50378	0.639	T	0.79517	-0.1771	10	0.59425	D	0.04	.	12.2462	0.54572	0.0:0.0:0.8298:0.1702	.	611	P42680	TEC_HUMAN	Y	611	ENSP00000370912:S611Y	ENSP00000370912:S611Y	S	-	2	0	TEC	47834254	0.996000	0.38824	1.000000	0.80357	0.146000	0.21551	4.049000	0.57397	2.441000	0.82636	0.591000	0.81541	TCT		0.438	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			
TEC	7006	hgsc.bcm.edu;ucsc.edu	37	4	48139499	48139499	+	Silent	SNP	A	A	G			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr4:48139499A>G	ENST00000381501.3	-	18	1987	c.1830T>C	c.(1828-1830)ccT>ccC	p.P610P		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						CTTCGAAAGAAGGCCTTCCCT	0.443																																																	0													110.0	103.0	105.0					4																	48139499		2203	4300	6503	SO:0001819	synonymous_variant	100124696			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1830T>C	4.37:g.48139499A>G			B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																				0.443	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			
TFR2	7036	hgsc.bcm.edu;ucsc.edu	37	7	100218519	100218519	+	Silent	SNP	C	C	G	rs374766778	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr7:100218519C>G	ENST00000462107.1	-	19	2654	c.2367G>C	c.(2365-2367)gcG>gcC	p.A789A	TFR2_ENST00000223051.3_Silent_p.A789A|TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000544242.1_Silent_p.A330A			Q9UP52	TFR2_HUMAN	transferrin receptor 2	789					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	CCCCGCTAAGCGCATTGGCTG	0.632																																																	0													52.0	47.0	49.0					7																	100218519		2203	4300	6503	SO:0001819	synonymous_variant	7036			AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.2367G>C	7.37:g.100218519C>G			A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																				0.632	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3		NM_003227	
EMC4	51234	hgsc.bcm.edu;ucsc.edu	37	15	34520009	34520009	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr15:34520009C>T	ENST00000267750.4	+	3	433	c.317C>T	c.(316-318)gCc>gTc	p.A106V	EMC4_ENST00000249209.4_Missense_Mutation_p.A106V|EMC4_ENST00000557879.1_Intron|EMC4_ENST00000559078.1_Intron|EMC4_ENST00000559421.1_Intron	NM_016454.2	NP_057538.1	Q5J8M3	EMC4_HUMAN	ER membrane protein complex subunit 4	106					apoptotic process (GO:0006915)	ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											TGTATGATGGCCTGGCGACCC	0.458																																																	0													161.0	138.0	146.0					15																	34520009		2201	4298	6499	SO:0001583	missense	0			BC016348	CCDS10035.1, CCDS66732.1	15q14	2012-05-23	2012-05-23	2012-05-23	ENSG00000128463	ENSG00000128463			28032	protein-coding gene	gene with protein product			"""transmembrane protein 85"""	TMEM85		18586032, 22119785	Standard	NM_001286420		Approved	FLJ90746, MGC24415, PIG17	uc001zhq.3	Q5J8M3	OTTHUMG00000129411	ENST00000267750.4:c.317C>T	15.37:g.34520009C>T	ENSP00000267750:p.Ala106Val		A8K3A9|B4DJQ4|Q96KX9|Q9BUI5|Q9P0T9	Missense_Mutation	SNP	ENST00000267750.4	37	CCDS10035.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100206	0.76983	.	.	ENSG00000128463	ENST00000267750;ENST00000249209	T;T	0.37915	1.17;1.17	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	N	0.02802	-0.49	0.80722	D	1	P;B	0.51351	0.944;0.005	P;B	0.48270	0.572;0.033	T	0.16158	-1.0412	10	0.16420	T	0.52	.	19.3845	0.94551	0.0:1.0:0.0:0.0	.	106;106	Q5J8M3-2;Q5J8M3	.;TMM85_HUMAN	V	106	ENSP00000267750:A106V;ENSP00000249209:A106V	ENSP00000249209:A106V	A	+	2	0	TMEM85	32307301	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.169000	0.64984	2.876000	0.98609	0.655000	0.94253	GCC		0.458	EMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251568.1		NM_016454	
USP2	9099	hgsc.bcm.edu;ucsc.edu	37	11	119229755	119229755	+	Missense_Mutation	SNP	G	G	T			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr11:119229755G>T	ENST00000260187.2	-	6	1445	c.1151C>A	c.(1150-1152)cCt>cAt	p.P384H	USP2_ENST00000525735.1_Missense_Mutation_p.P175H|USP2_ENST00000455332.2_Missense_Mutation_p.P141H	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	384	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GAGGTTCTCAGGGTTGGACTT	0.473																																																	0													101.0	91.0	94.0					11																	119229755		2199	4295	6494	SO:0001583	missense	9099			AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.1151C>A	11.37:g.119229755G>T	ENSP00000260187:p.Pro384His		B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	ENST00000260187.2	37	CCDS8422.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.594301	0.28445	.	.	ENSG00000036672	ENST00000455332;ENST00000260187;ENST00000392808;ENST00000525735	T;T;T	0.02890	4.12;4.12;4.12	5.92	4.99	0.66335	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.584559	0.18692	N	0.133836	T	0.04003	0.0112	L	0.48877	1.53	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.28933	-1.0028	10	0.51188	T	0.08	-0.4775	10.7447	0.46172	0.0:0.1428:0.709:0.1482	.	141;384;175	E9PPM2;O75604;O75604-4	.;UBP2_HUMAN;.	H	141;384;131;175	ENSP00000407842:P141H;ENSP00000260187:P384H;ENSP00000436952:P175H	ENSP00000260187:P384H	P	-	2	0	USP2	118734965	0.000000	0.05858	0.147000	0.22382	0.988000	0.76386	0.657000	0.24963	1.458000	0.47871	0.655000	0.94253	CCT		0.473	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2		NM_171997	
USP6NL	9712	hgsc.bcm.edu;ucsc.edu	37	10	11504703	11504703	+	Missense_Mutation	SNP	T	T	C			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr10:11504703T>C	ENST00000609104.1	-	15	2618	c.2224A>G	c.(2224-2226)Aca>Gca	p.T742A	USP6NL_ENST00000277575.5_Missense_Mutation_p.T759A|USP6NL_ENST00000379237.2_Missense_Mutation_p.T765A	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	742					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						GGTCTGTATGTATAACTAACT	0.458																																																	0													126.0	129.0	128.0					10																	11504703		1953	4149	6102	SO:0001583	missense	9712			BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.2224A>G	10.37:g.11504703T>C	ENSP00000476462:p.Thr742Ala		A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	T	2.598	-0.293546	0.05568	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.04015	3.73;3.74	6.17	-0.772	0.10998	.	0.360626	0.27323	N	0.019896	T	0.03915	0.0110	L	0.54323	1.7	0.09310	N	1	B;B	0.22146	0.022;0.065	B;B	0.21708	0.016;0.036	T	0.39014	-0.9634	10	0.23891	T	0.37	.	1.7815	0.03032	0.1088:0.1879:0.2254:0.478	.	742;759	Q92738;Q92738-2	US6NL_HUMAN;.	A	742;759;742	ENSP00000277575:T759A;ENSP00000368539:T742A	ENSP00000277575:T759A	T	-	1	0	USP6NL	11544709	0.032000	0.19561	0.000000	0.03702	0.016000	0.09150	0.073000	0.14640	-0.059000	0.13154	0.533000	0.62120	ACA		0.458	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3		NM_014688	
VSIG10	54621	hgsc.bcm.edu;ucsc.edu	37	12	118511660	118511677	+	In_Frame_Del	DEL	TGATCACCTCGGGCTGGG	TGATCACCTCGGGCTGGG	-	rs76814182|rs569997181|rs142627542|rs540996271	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	TGATCACCTCGGGCTGGG	TGATCACCTCGGGCTGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr12:118511660_118511677delTGATCACCTCGGGCTGGG	ENST00000359236.5	-	5	1322_1339	c.1046_1063delCCCAGCCCGAGGTGATCA	c.(1045-1065)acccagcccgaggtgatcatc>atc	p.TQPEVI349del		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	349	Ig-like C2-type 4.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CTAGGCTGGATGATCACCTCGGGCTGGGTAAGGTTCCT	0.583														26	0.00519169	0.0008	0.0072	5008	,	,		21969	0.0		0.0179	False		,,,				2504	0.002																0										16,3866		2,12,1927						4.4	0.9		dbSNP_134	58	206,7786		8,190,3798	no	coding	VSIG10	NM_019086.5		10,202,5725	A1A1,A1R,RR		2.5776,0.4122,1.8696				222,11652				SO:0001651	inframe_deletion	54621				CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1046_1063delCCCAGCCCGAGGTGATCA	12.37:g.118511660_118511677delTGATCACCTCGGGCTGGG	ENSP00000352172:p.Thr349_Ile354del		Q9NWQ7	In_Frame_Del	DEL	ENST00000359236.5	37	CCDS44992.1																																																																																				0.583	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2		NM_019086	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786681	75786681	+	Missense_Mutation	SNP	G	G	A	rs111677009	byFrequency	TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr3:75786681G>A	ENST00000478296.1	-	4	2219	c.1943C>T	c.(1942-1944)cCg>cTg	p.P648L	ZNF717_ENST00000400845.3_Missense_Mutation_p.P691L|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.P698L|ZNF717_ENST00000477374.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GCTTTTCCCCGGTGTGAGTTC	0.408																																																	0													4.0	4.0	4.0					3																	75786681		561	1392	1953	SO:0001583	missense	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1943C>T	3.37:g.75786681G>A	ENSP00000419377:p.Pro648Leu			Missense_Mutation	SNP	ENST00000478296.1	37		.	.	.	.	.	.	.	.	.	.	.	5.989	0.366403	0.11352	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.05580	3.42;3.55;3.54	1.27	-2.53	0.06326	.	.	.	.	.	T	0.01627	0.0052	N	0.00525	-1.395	0.34331	P	0.31233	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	8	0.87932	D	0	.	3.1326	0.06429	0.3655:0.0:0.1987:0.4358	.	698	C9JSV9	.	L	648;698;691	ENSP00000419377:P648L;ENSP00000409514:P698L;ENSP00000383643:P691L	ENSP00000383643:P691L	P	-	2	0	ZNF717	75869371	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-7.316000	0.00039	-1.950000	0.01030	-3.190000	0.00055	CCG		0.408	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2		NM_001128223	
ZNF831	128611	hgsc.bcm.edu	37	20	57769147	57769147	+	Missense_Mutation	SNP	G	G	A			TCGA-DV-5575-01A-01D-1534-10	TCGA-DV-5575-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	eb2d0a1a-b684-484a-86a4-bd40c8ac7ce8	bf9f5144-b35f-493d-b2b0-e4ebbe29fe88	g.chr20:57769147G>A	ENST00000371030.2	+	1	3073	c.3073G>A	c.(3073-3075)Gac>Aac	p.D1025N		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1025							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GTTGGGGGGGGACAAGGGGGA	0.682																																																	0													20.0	23.0	22.0					20																	57769147		2003	4185	6188	SO:0001583	missense	128611			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3073G>A	20.37:g.57769147G>A	ENSP00000360069:p.Asp1025Asn		Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.027571	0.35797	.	.	ENSG00000124203	ENST00000371030	T	0.06933	3.24	4.49	3.52	0.40303	.	0.911342	0.09308	N	0.819957	T	0.06872	0.0175	N	0.19112	0.55	0.09310	N	1	B	0.29432	0.244	B	0.26770	0.073	T	0.38757	-0.9646	10	0.38643	T	0.18	-4.3528	11.5227	0.50560	0.0:0.3468:0.6532:0.0	.	1025	Q5JPB2	ZN831_HUMAN	N	1025	ENSP00000360069:D1025N	ENSP00000360069:D1025N	D	+	1	0	ZNF831	57202542	0.140000	0.22579	0.008000	0.14137	0.017000	0.09413	1.887000	0.39698	0.987000	0.38709	0.411000	0.27672	GAC		0.682	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2		NM_178457	
