#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
ZNF778	197320	broad.mit.edu	37	16	89293578	89293578	+	Silent	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr16:89293578C>T	ENST00000433976.2	+	6	1130	c.798C>T	c.(796-798)gcC>gcT	p.A266A	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.A224A	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GGTACACTGCCTACCTTACTG	0.527																																						ENST00000433976.2																			0				endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24						c.(796-798)gcC>gcT		zinc finger protein 778							72.0	72.0	72.0					16																	89293578		2060	4208	6268	SO:0001819	synonymous_variant	197320				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr16:89293578C>T	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.798C>T	16.37:g.89293578C>T						RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.A224A	p.A266A	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0269)	6	1130	+			266					Q08AG0	Silent	SNP	ENST00000433976.2	37	c.798C>T	CCDS45550.1																																																																																				0.527	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		4	85	0	0	0	1	0	4	85				
RGPD3	653489	broad.mit.edu	37	2	107049631	107049631	+	Silent	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr2:107049631C>T	ENST00000409886.3	-	16	2403	c.2316G>A	c.(2314-2316)gcG>gcA	p.A772A	RGPD3_ENST00000304514.7_Silent_p.A772A	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	772					protein targeting to Golgi (GO:0000042)			p.A772A(4)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTTCTGAATCCGCATTTCGCA	0.373																																						ENST00000409886.3																			4	Substitution - coding silent(4)	p.A772A(4)	kidney(2)|endometrium(2)	breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						c.(2314-2316)gcG>gcA		RANBP2-like and GRIP domain containing 3							81.0	68.0	72.0					2																	107049631		692	1590	2282	SO:0001819	synonymous_variant	653489				intracellular transport		binding	g.chr2:107049631C>T		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2316G>A	2.37:g.107049631C>T						RGPD3_ENST00000304514.7_Silent_p.A772A	p.A772A	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN			16	2403	-			772					B8ZZM4	Silent	SNP	ENST00000409886.3	37	c.2316G>A	CCDS46379.1																																																																																				0.373	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		5	380	0	0	0	1	0	5	380				
BMS1P20	96610	broad.mit.edu	37	22	22663086	22663086	+	RNA	SNP	T	T	G	rs1054157|rs71318762	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr22:22663086T>G	ENST00000426066.1	+	0	525					NR_027293.1				BMS1 pseudogene 20																		AGCTGCCACATAAGTTGTCCT	0.299													.|||	3161	0.63119	0.9652	0.4726	5008	,	,		9186	0.4077		0.5219	False		,,,				2504	0.635					ENST00000426066.1																			0																																																			0							g.chr22:22663086T>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663086T>G								NR_027293.1						0	525	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.299	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	42	0	0	0	1	0	4	42				
TRAJ24	28731	broad.mit.edu	37	14	22991074	22991074	+	RNA	SNP	A	A	G			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr14:22991074A>G	ENST00000390513.1	+	0	63				TRAJ21_ENST00000390516.1_RNA|TRAJ22_ENST00000390515.1_RNA|TRAJ23_ENST00000390514.1_RNA|TRAJ20_ENST00000390517.1_RNA					T cell receptor alpha joining 24																		TGACTGTTTTACCTGGTAGGC	0.403																																						ENST00000390515.1																			0																				314.0	293.0	299.0					14																	22991074		1876	4105	5981			0							g.chr14:22991074A>G	X02887		14q11.2	2012-02-07			ENSG00000211865	ENSG00000211865		"""T cell receptors / TRA locus"""	12053	other	T cell receptor gene						2993909, 8188290	Standard	NG_001332		Approved				OTTHUMG00000170943		14.37:g.22991074A>G														0	59	+									RNA	SNP	ENST00000390513.1	37																																																																																						0.403	TRAJ24-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	TR_J_gene	TR_J_gene	OTTHUMT00000410974.1	NG_001332		131	258	0	0	0	1	0	131	258				
HMGB3	3149	broad.mit.edu	37	X	150156360	150156360	+	Silent	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chrX:150156360G>A	ENST00000325307.7	+	5	672	c.576G>A	c.(574-576)gaG>gaA	p.E192E	HMGB3_ENST00000448905.2_Silent_p.E192E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	192	Asp/Glu-rich (acidic).				DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.E192E(1)		endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					aggaagaagaggaggaggagg	0.443																																						ENST00000325307.7																			1	Substitution - coding silent(1)	p.E192E(1)	large_intestine(1)	endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8						c.(574-576)gaG>gaA		high mobility group box 3							50.0	48.0	49.0					X																	150156360		2202	4299	6501	SO:0001819	synonymous_variant	3149				DNA recombination|multicellular organismal development	chromosome|nucleus	DNA bending activity|double-stranded DNA binding	g.chrX:150156360G>A	AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"""High-mobility group / Canonical"""	5004	protein-coding gene	gene with protein product	"""non-histone chromosomal protein"""	300193	"""high-mobility group (nonhistone chromosomal) protein 4"", ""high-mobility group box 3"""	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.576G>A	X.37:g.150156360G>A						HMGB3_ENST00000448905.2_Silent_p.E192E	p.E192E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN			5	672	+	Acute lymphoblastic leukemia(192;6.56e-05)		192			Asp/Glu-rich (acidic).		O95556|Q6NS40	Silent	SNP	ENST00000325307.7	37	c.576G>A	CCDS35428.1																																																																																				0.443	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342		4	58	0	0	0	1	0	4	58				
PTPN13	5783	broad.mit.edu	37	4	87696669	87696669	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:87696669G>A	ENST00000411767.2	+	35	5818	c.5755G>A	c.(5755-5757)Gca>Aca	p.A1919T	PTPN13_ENST00000316707.6_Missense_Mutation_p.A1728T|PTPN13_ENST00000436978.1_Missense_Mutation_p.A1924T|PTPN13_ENST00000427191.2_Missense_Mutation_p.A1900T|PTPN13_ENST00000511467.1_Missense_Mutation_p.A1924T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1919	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		AAGGTCCGTCGCAGCCATTGA	0.383																																						ENST00000436978.1																			0				NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93						c.(5770-5772)Gca>Aca		protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)							85.0	86.0	86.0					4																	87696669		2129	4258	6387	SO:0001583	missense	0					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein tyrosine phosphatase activity	g.chr4:87696669G>A		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5755G>A	4.37:g.87696669G>A	ENSP00000407249:p.Ala1919Thr					PTPN13_ENST00000427191.2_Missense_Mutation_p.A1900T|PTPN13_ENST00000316707.6_Missense_Mutation_p.A1728T|PTPN13_ENST00000411767.2_Missense_Mutation_p.A1919T|PTPN13_ENST00000511467.1_Missense_Mutation_p.A1924T	p.A1924T	NM_080683.2|NM_080685.2	NP_542414.1|NP_542416.1	Q12923	PTN13_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00082)	35	6250	+		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)	1919			PDZ 5.		B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	c.5770G>A	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227751	0.79576	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.45	5.45	0.79879	PDZ/DHR/GLGF (4);	0.000000	0.48767	D	0.000179	D	0.85234	0.5650	M	0.93638	3.44	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.999;1.0;0.999	D	0.88914	0.3361	10	0.87932	D	0	.	19.2786	0.94042	0.0:0.0:1.0:0.0	.	1728;1900;1919;1924	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	1900;1924;1728;1919;1924;1868	ENSP00000408368:A1900T;ENSP00000394794:A1924T;ENSP00000322675:A1728T;ENSP00000407249:A1919T;ENSP00000426626:A1924T	ENSP00000322675:A1728T	A	+	1	0	PTPN13	87915693	1.000000	0.71417	0.810000	0.32431	0.271000	0.26615	8.930000	0.92872	2.552000	0.86080	0.460000	0.39030	GCA		0.383	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			6	31	0	0	0	1	0	6	31				
KRT28	162605	broad.mit.edu	37	17	38950240	38950240	+	Missense_Mutation	SNP	G	G	A	rs150448547		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:38950240G>A	ENST00000306658.7	-	6	1102	c.1037C>T	c.(1036-1038)gCg>gTg	p.A346V		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				CTGGATCTGCGCCAGCTGCGT	0.577																																					Melanoma(19;789 869 15380 26882 39836)	ENST00000306658.7																			0				NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30						c.(1036-1038)gCg>gTg		keratin 28		G	VAL/ALA	0,4406		0,0,2203	132.0	135.0	134.0		1037	5.7	1.0	17	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT28	NM_181535.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	346/465	38950240	1,13005	2203	4300	6503	SO:0001583	missense	162605					cytoplasm|intermediate filament	structural molecule activity	g.chr17:38950240G>A	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.1037C>T	17.37:g.38950240G>A	ENSP00000305263:p.Ala346Val						p.A346V	NM_181535.3	NP_853513.2	Q7Z3Y7	K1C28_HUMAN			6	1102	-		Breast(137;0.000301)	346			Coil 2.|Rod.			Missense_Mutation	SNP	ENST00000306658.7	37	c.1037C>T	CCDS11376.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.251696	0.80135	0.0	1.16E-4	ENSG00000173908	ENST00000306658	D	0.88896	-2.44	5.7	5.7	0.88788	Filament (1);	0.103006	0.43260	D	0.000597	D	0.88544	0.6465	M	0.65320	2	0.22737	N	0.998797	P	0.51653	0.947	B	0.43658	0.426	D	0.84850	0.0813	10	0.72032	D	0.01	.	15.618	0.76784	0.0:0.0:0.8622:0.1378	.	346	Q7Z3Y7	K1C28_HUMAN	V	346	ENSP00000305263:A346V	ENSP00000305263:A346V	A	-	2	0	KRT28	36203766	0.000000	0.05858	0.995000	0.50966	0.991000	0.79684	0.689000	0.25437	2.846000	0.97976	0.650000	0.86243	GCG		0.577	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535		15	275	0	0	0	1	0	15	275				
CEL	1056	broad.mit.edu	37	9	135946995	135946995	+	Silent	SNP	C	C	T	rs374403885	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr9:135946995C>T	ENST00000372080.4	+	11	2131	c.2115C>T	c.(2113-2115)ccC>ccT	p.P705P	CEL_ENST00000351304.7_Silent_p.P636P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	702	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		GGGCCCCCCCCGTGACCCCCA	0.816													C|||	72	0.014377	0.0053	0.0072	5008	,	,		4342	0.003		0.008	False		,,,				2504	0.0501					ENST00000372080.4																			0				NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20						c.(2113-2115)ccC>ccT		carboxyl ester lipase							2.0	3.0	3.0					9																	135946995		1207	2829	4036	SO:0001819	synonymous_variant	1056				cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity	g.chr9:135946995C>T	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2115C>T	9.37:g.135946995C>T						CEL_ENST00000351304.7_Silent_p.P636P	p.P705P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)	11	2131	+			702			17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).		Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	37	c.2115C>T	CCDS43896.1																																																																																				0.816	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			3	8	0	0	0	1	0	3	8				
MUC7	4589	broad.mit.edu	37	4	71347240	71347240	+	Missense_Mutation	SNP	T	T	C	rs145745951	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:71347240T>C	ENST00000304887.5	+	3	969	c.779T>C	c.(778-780)gTc>gCc	p.V260A	MUC7_ENST00000456088.1_Missense_Mutation_p.V260A|MUC7_ENST00000413702.1_Missense_Mutation_p.V260A	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	260	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.V260A(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACCACAGCTGTCCCACCCACA	0.587													C|||	16	0.00319489	0.0038	0.0029	5008	,	,		19991	0.0		0.008	False		,,,				2504	0.001					ENST00000413702.1																			1	Substitution - Missense(1)	p.V260A(1)	skin(1)	central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(778-780)gTc>gCc		mucin 7, secreted							521.0	441.0	468.0					4																	71347240		2201	4300	6501	SO:0001583	missense	4589					extracellular region	protein binding	g.chr4:71347240T>C	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.779T>C	4.37:g.71347240T>C	ENSP00000302021:p.Val260Ala					MUC7_ENST00000456088.1_Missense_Mutation_p.V260A|MUC7_ENST00000304887.5_Missense_Mutation_p.V260A	p.V260A	NM_001145006.1	NP_001138478.1	Q8TAX7	MUC7_HUMAN	Lung(101;0.211)		4	1067	+			260			Thr-rich.		Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	c.779T>C	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.737530	0.00681	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.44482	0.92;0.92;0.92	1.11	-2.23	0.06930	.	.	.	.	.	T	0.13543	0.0328	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20438	-1.0275	8	.	.	.	.	3.5881	0.07978	0.0:0.2514:0.2169:0.5317	.	260	Q8TAX7	MUC7_HUMAN	A	260	ENSP00000407422:V260A;ENSP00000400585:V260A;ENSP00000302021:V260A	.	V	+	2	0	MUC7	71381829	0.000000	0.05858	0.003000	0.11579	0.040000	0.13550	-0.078000	0.11375	-1.146000	0.02854	-0.330000	0.08379	GTC		0.587	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		11	277	0	0	0	1	0	11	277				
ZFP64	55734	broad.mit.edu	37	20	50701174	50701174	+	Silent	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr20:50701174G>A	ENST00000361387.2	-	9	1920	c.1860C>T	c.(1858-1860)agC>agT	p.S620S	ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371523.4_Silent_p.S401S	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CCGAGGCACCGCTTTCCGGTG	0.597																																						ENST00000361387.2																			0				breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						c.(1858-1860)agC>agT		ZFP64 zinc finger protein							53.0	51.0	52.0					20																	50701174		2203	4300	6503	SO:0001819	synonymous_variant	55734				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr20:50701174G>A	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1860C>T	20.37:g.50701174G>A						ZFP64_ENST00000371523.4_Silent_p.S401S|ZFP64_ENST00000371518.2_Intron	p.S620S	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN			9	1920	-			465					Q9NTS7|Q9NVH4	Silent	SNP	ENST00000361387.2	37	c.1860C>T	CCDS13439.1																																																																																				0.597	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		24	43	0	0	0	1	0	24	43				
IRF7	3665	broad.mit.edu	37	11	615146	615146	+	Missense_Mutation	SNP	T	T	G			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr11:615146T>G	ENST00000397574.2	-	3	503	c.134A>C	c.(133-135)aAg>aCg	p.K45T	IRF7_ENST00000525445.1_5'UTR|IRF7_ENST00000397562.3_5'UTR|IRF7_ENST00000397570.1_Missense_Mutation_p.K45T|IRF7_ENST00000330243.5_Missense_Mutation_p.K58T|IRF7_ENST00000397566.1_Missense_Mutation_p.K58T|IRF7_ENST00000348655.6_Missense_Mutation_p.K45T	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	45					cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGCGAAGTGCTTCCAGGGCAC	0.697																																						ENST00000397566.1																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						c.(172-174)aAg>aCg		interferon regulatory factor 7							10.0	12.0	11.0					11																	615146		2137	4206	6343	SO:0001583	missense	3665				interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of interferon-alpha production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr11:615146T>G	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.134A>C	11.37:g.615146T>G	ENSP00000380704:p.Lys45Thr					IRF7_ENST00000397562.3_5'UTR|IRF7_ENST00000330243.5_Missense_Mutation_p.K58T|IRF7_ENST00000348655.6_Missense_Mutation_p.K45T|IRF7_ENST00000525445.1_5'UTR|IRF7_ENST00000397574.2_Missense_Mutation_p.K45T|IRF7_ENST00000397570.1_Missense_Mutation_p.K45T	p.K58T	NM_004031.2	NP_004022.2	Q92985	IRF7_HUMAN		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	1	582	-		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)	45					B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Missense_Mutation	SNP	ENST00000397574.2	37	c.173A>C	CCDS7703.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001131	0.74818	.	.	ENSG00000185507	ENST00000348655;ENST00000397570;ENST00000397566;ENST00000397574;ENST00000330243	D;D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86;-4.86	4.43	3.29	0.37713	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.117488	0.56097	D	0.000035	D	0.98488	0.9496	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.98290	1.0513	10	0.87932	D	0	-36.998	8.0712	0.30691	0.0:0.0944:0.0:0.9056	.	45;45;58	Q92985-2;Q92985;Q92985-4	.;IRF7_HUMAN;.	T	45;45;58;45;58	ENSP00000331803:K45T;ENSP00000380700:K45T;ENSP00000380697:K58T;ENSP00000380704:K45T;ENSP00000329411:K58T	ENSP00000329411:K58T	K	-	2	0	IRF7	605146	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	4.194000	0.58393	0.668000	0.31126	0.402000	0.26972	AAG		0.697	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572		6	14	0	0	0	1	0	6	14				
CIC	23152	broad.mit.edu	37	19	42799050	42799050	+	Missense_Mutation	SNP	C	C	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr19:42799050C>A	ENST00000575354.2	+	20	4574	c.4534C>A	c.(4534-4536)Cgt>Agt	p.R1512S	CIC_ENST00000160740.3_Missense_Mutation_p.R1510S|CIC_ENST00000572681.2_Missense_Mutation_p.R2418S	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GTTGAAGATCCGTGAGGTGCG	0.632			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(7252-7254)Cgt>Agt		capicua transcriptional repressor							52.0	52.0	52.0					19																	42799050		2203	4300	6503	SO:0001583	missense	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42799050C>A	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4534C>A	19.37:g.42799050C>A	ENSP00000458663:p.Arg1512Ser					CIC_ENST00000575354.2_Missense_Mutation_p.R1512S|CIC_ENST00000160740.3_Missense_Mutation_p.R1510S	p.R2418S			Q96RK0	CIC_HUMAN			21	7320	+		Prostate(69;0.00682)	1512					Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	c.7252C>A	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.330104	0.60743	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	3.37	0.38596	.	.	.	.	.	T	0.62514	0.2434	L	0.29908	0.895	0.40778	D	0.983142	D	0.65815	0.995	D	0.70227	0.968	T	0.65998	-0.6032	8	0.87932	D	0	-6.0224	11.7222	0.51689	0.1768:0.8232:0.0:0.0	.	1512	Q96RK0	CIC_HUMAN	S	1512	.	ENSP00000160740:R1512S	R	+	1	0	CIC	47490890	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.911000	0.48774	2.513000	0.84729	0.491000	0.48974	CGT		0.632	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			32	42	1	0	2.75727e-19	1	3.06364e-19	32	42				
ANKRD17	26057	broad.mit.edu	37	4	73957008	73957008	+	Nonsense_Mutation	SNP	C	C	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:73957008C>A	ENST00000358602.4	-	29	6453	c.6337G>T	c.(6337-6339)Gga>Tga	p.G2113*	ANKRD17_ENST00000330838.6_Nonsense_Mutation_p.G1862*|ANKRD17_ENST00000509867.2_Nonsense_Mutation_p.G2000*	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2113					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAAACAGATCCCGGAGGTTGT	0.483																																						ENST00000358602.4																			0				NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96						c.(6337-6339)Gga>Tga		ankyrin repeat domain 17							158.0	161.0	160.0					4																	73957008		2203	4300	6503	SO:0001587	stop_gained	26057				interspecies interaction between organisms	cytoplasm|nucleus	RNA binding	g.chr4:73957008C>A	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6337G>T	4.37:g.73957008C>A	ENSP00000351416:p.Gly2113*					ANKRD17_ENST00000509867.2_Nonsense_Mutation_p.G2000*|ANKRD17_ENST00000330838.6_Nonsense_Mutation_p.G1862*	p.G2113*	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		29	6453	-	Breast(15;0.000295)		2113					E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Nonsense_Mutation	SNP	ENST00000358602.4	37	c.6337G>T	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	C	45	11.705230	0.99593	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000426917	.	.	.	4.97	4.97	0.65823	.	0.194484	0.35970	N	0.002862	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	9.177	0.37118	0.0:0.8405:0.0:0.1595	.	.	.	.	X	2113;1520;1862;2000;497	.	ENSP00000332265:G1862X	G	-	1	0	ANKRD17	74175872	0.708000	0.27876	1.000000	0.80357	0.980000	0.70556	2.676000	0.46883	2.588000	0.87417	0.650000	0.86243	GGA		0.483	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		15	182	1	0	3.27435e-08	1	3.48335e-08	15	182				
TBC1D3P2	440452	broad.mit.edu	37	17	60342504	60342504	+	RNA	SNP	T	T	C	rs200286216		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:60342504T>C	ENST00000581291.1	-	0	1649									TBC1 domain family, member 3 pseudogene 2											breast(2)|kidney(1)|lung(2)	5						CAGTGCTGGGTGCACTGCAGG	0.637																																						ENST00000581291.1																			0				breast(2)|kidney(1)|lung(2)	5																																														0							g.chr17:60342504T>C			17q23.2	2009-05-14				ENSG00000188755			27783	pseudogene	pseudogene							Standard	NR_027486		Approved		uc002izq.2				17.37:g.60342504T>C														0	1649	-									RNA	SNP	ENST00000581291.1	37																																																																																						0.637	TBC1D3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445021.1	NR_027486		6	141	0	0	0	1	0	6	141				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			8	75	0	0	0	1	0	8	75				
ARFIP2	23647	broad.mit.edu	37	11	6501609	6501609	+	Missense_Mutation	SNP	G	G	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr11:6501609G>T	ENST00000254584.2	-	2	126	c.43C>A	c.(43-45)Cct>Act	p.P15T	TIMM10B_ENST00000472836.1_5'Flank|ARFIP2_ENST00000423813.2_Intron|ARFIP2_ENST00000445086.2_Intron|TIMM10B_ENST00000254616.6_5'Flank|ARFIP2_ENST00000396777.3_Missense_Mutation_p.P15T|TIMM10B_ENST00000530751.1_5'Flank|ARFIP2_ENST00000525235.1_Missense_Mutation_p.P15T	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	15					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCGTGGATAGGGATCTCCATT	0.517																																					Melanoma(119;796 1674 9049 20480 24794)	ENST00000254584.2																			0				endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15						c.(43-45)Cct>Act		ADP-ribosylation factor interacting protein 2							68.0	58.0	61.0					11																	6501609		2201	4296	6497	SO:0001583	missense	23647				actin cytoskeleton organization|cellular component movement|lamellipodium assembly|ruffle organization|small GTPase mediated signal transduction	cell cortex|plasma membrane|ruffle	GTP binding|GTP-dependent protein binding|Rac GTPase binding	g.chr11:6501609G>T	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"""arfaptin 2"""	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.43C>A	11.37:g.6501609G>T	ENSP00000254584:p.Pro15Thr					ARFIP2_ENST00000445086.2_Intron|ARFIP2_ENST00000423813.2_Intron|ARFIP2_ENST00000525235.1_Missense_Mutation_p.P15T|ARFIP2_ENST00000396777.3_Missense_Mutation_p.P15T	p.P15T	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	2	126	-		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)	15					B4DX86|B4E306|D3DQT5	Missense_Mutation	SNP	ENST00000254584.2	37	c.43C>A	CCDS7765.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114793	0.77210	.	.	ENSG00000132254	ENST00000254584;ENST00000396777;ENST00000525235	T;T	0.81247	-1.47;-1.47	5.08	5.08	0.68730	.	0.120183	0.64402	D	0.000020	D	0.88020	0.6325	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	D	0.88122	0.2832	10	0.49607	T	0.09	.	16.2472	0.82450	0.0:0.0:1.0:0.0	.	15;15;15	B4DUZ3;E9PPY7;P53365	.;.;ARFP2_HUMAN	T	15	ENSP00000254584:P15T;ENSP00000379998:P15T	ENSP00000254584:P15T	P	-	1	0	ARFIP2	6458185	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.106000	0.89555	2.363000	0.80096	0.561000	0.74099	CCT		0.517	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402		13	27	1	0	0.000308642	1	0.000321502	13	27				
LOC101927079	101927079	broad.mit.edu	37	15	22332492	22332492	+	RNA	SNP	A	A	C	rs540968052		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr15:22332492A>C	ENST00000558896.1	+	0	299																											TATTTCTCTTATTACTATTTT	0.383																																						ENST00000558896.1																			0																																																			0							g.chr15:22332492A>C																													15.37:g.22332492A>C														0	299	+									RNA	SNP	ENST00000558896.1	37																																																																																						0.383	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000417625.1			5	210	0	0	0	1	0	5	210				
IQGAP2	10788	broad.mit.edu	37	5	75967776	75967776	+	Silent	SNP	G	G	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr5:75967776G>T	ENST00000274364.6	+	24	3333	c.3036G>T	c.(3034-3036)gtG>gtT	p.V1012V	IQGAP2_ENST00000396234.3_Silent_p.V508V|IQGAP2_ENST00000502745.1_Silent_p.V508V|IQGAP2_ENST00000379730.3_Silent_p.V514V	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1012	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AGGCTTGGGTGAACCAACTAG	0.433																																						ENST00000274364.6																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68						c.(3034-3036)gtG>gtT		IQ motif containing GTPase activating protein 2							48.0	51.0	50.0					5																	75967776		2203	4300	6503	SO:0001819	synonymous_variant	10788				small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity	g.chr5:75967776G>T	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3036G>T	5.37:g.75967776G>T						IQGAP2_ENST00000502745.1_Silent_p.V508V|IQGAP2_ENST00000379730.3_Silent_p.V514V|IQGAP2_ENST00000396234.3_Silent_p.V508V	p.V1012V	NM_006633.2	NP_006624.2	Q13576	IQGA2_HUMAN		all cancers(79;1.38e-36)	24	3333	+		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)	1012			Ras-GAP.		A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	c.3036G>T	CCDS34188.1																																																																																				0.433	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		16	14	1	0	6.94344e-10	1	7.54722e-10	16	14				
ABCF3	55324	broad.mit.edu	37	3	183908941	183908941	+	Silent	SNP	G	G	A	rs182234232	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr3:183908941G>A	ENST00000429586.2	+	16	1652	c.1467G>A	c.(1465-1467)ccG>ccA	p.P489P	EIF2B5_ENST00000444495.1_Intron|ABCF3_ENST00000292808.5_Silent_p.P483P	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	489					defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGTTCTCGCCGCCAATTCTGC	0.567													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18458	0.0		0.0	False		,,,				2504	0.0					ENST00000429586.2																			0				breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39						c.(1465-1467)ccG>ccA		ATP-binding cassette, sub-family F (GCN20), member 3		G		1,4405	4.2+/-10.8	0,1,2202	154.0	146.0	149.0		1467	-5.9	0.7	3		149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ABCF3	NM_018358.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		489/710	183908941	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	55324						ATP binding|ATPase activity	g.chr3:183908941G>A	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1467G>A	3.37:g.183908941G>A						ABCF3_ENST00000292808.5_Silent_p.P483P|EIF2B5_ENST00000444495.1_Intron	p.P489P	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		16	1652	+	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		489					A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Silent	SNP	ENST00000429586.2	37	c.1467G>A	CCDS3254.1																																																																																				0.567	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358		5	180	0	0	0	1	0	5	180				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			37	52	0	0	0	1	0	37	52				
ABLIM2	84448	broad.mit.edu	37	4	8055951	8055951	+	Silent	SNP	C	C	T	rs371704121		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:8055951C>T	ENST00000341937.5	-	8	850	c.786G>A	c.(784-786)gcG>gcA	p.A262A	ABLIM2_ENST00000318888.4_Silent_p.A19A|ABLIM2_ENST00000546334.1_Silent_p.A262A|ABLIM2_ENST00000505872.1_Silent_p.A262A|ABLIM2_ENST00000428004.2_Silent_p.A262A|ABLIM2_ENST00000545242.1_Silent_p.A262A|ABLIM2_ENST00000296372.8_Silent_p.A262A|ABLIM2_ENST00000407564.3_Silent_p.A262A|ABLIM2_ENST00000361737.5_Silent_p.A262A|ABLIM2_ENST00000447017.2_Silent_p.A262A|ABLIM2_ENST00000361581.5_Silent_p.A262A|ABLIM2_ENST00000514025.1_Silent_p.A19A	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	262	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						CTTGTCGACACGCCGGATGCC	0.502																																						ENST00000318888.4																			0				NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						c.(55-57)gcG>gcA		actin binding LIM protein family, member 2							99.0	104.0	102.0					4																	8055951		2012	4192	6204	SO:0001819	synonymous_variant	84448				axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding	g.chr4:8055951C>T	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"""actin binding LIM protein 2"""				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.786G>A	4.37:g.8055951C>T						ABLIM2_ENST00000447017.2_Silent_p.A262A|ABLIM2_ENST00000428004.2_Silent_p.A262A|ABLIM2_ENST00000407564.3_Silent_p.A262A|ABLIM2_ENST00000361581.5_Silent_p.A262A|ABLIM2_ENST00000514025.1_Silent_p.A19A|ABLIM2_ENST00000361737.5_Silent_p.A262A|ABLIM2_ENST00000296372.8_Silent_p.A262A|ABLIM2_ENST00000545242.1_Silent_p.A262A|ABLIM2_ENST00000341937.5_Silent_p.A262A|ABLIM2_ENST00000546334.1_Silent_p.A262A|ABLIM2_ENST00000505872.1_Silent_p.A262A	p.A19A			Q6H8Q1	ABLM2_HUMAN			8	928	-			262					E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Silent	SNP	ENST00000341937.5	37	c.57G>A	CCDS47013.1																																																																																				0.502	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		15	46	0	0	0	1	0	15	46				
DSG4	147409	broad.mit.edu	37	18	28992950	28992950	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr18:28992950A>G	ENST00000308128.4	+	16	2650	c.2515A>G	c.(2515-2517)Aaa>Gaa	p.K839E	DSG4_ENST00000359747.4_Missense_Mutation_p.K858E|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	839					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TTTAGATCCAAAATTTAGGAC	0.448																																						ENST00000359747.4																			0				NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70						c.(2572-2574)Aaa>Gaa		desmoglein 4							140.0	131.0	134.0					18																	28992950		2203	4300	6503	SO:0001583	missense	147409				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding	g.chr18:28992950A>G	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2515A>G	18.37:g.28992950A>G	ENSP00000311859:p.Lys839Glu					RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000308128.4_Missense_Mutation_p.K839E	p.K858E	NM_001134453.1	NP_001127925.1	Q86SJ6	DSG4_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.00504)		15	2601	+			839					A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	c.2572A>G	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141029	0.77775	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.78126	-1.15;-1.15	5.64	5.64	0.86602	Cadherin, cytoplasmic domain (1);	.	.	.	.	D	0.87629	0.6225	M	0.75447	2.3	0.40531	D	0.980936	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88817	0.3296	9	0.54805	T	0.06	.	15.8549	0.78968	1.0:0.0:0.0:0.0	.	858;839	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	E	839;858	ENSP00000311859:K839E;ENSP00000352785:K858E	ENSP00000311859:K839E	K	+	1	0	DSG4	27246948	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.138000	0.77305	2.141000	0.66446	0.528000	0.53228	AAA		0.448	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		8	206	0	0	0	1	0	8	206				
BMS1P20	96610	broad.mit.edu	37	22	22663087	22663087	+	RNA	SNP	A	A	G	rs1054158|rs71318762	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr22:22663087A>G	ENST00000426066.1	+	0	526					NR_027293.1				BMS1 pseudogene 20																		GCTGCCACATAAGTTGTCCTT	0.303													.|||	3161	0.63119	0.9652	0.4726	5008	,	,		8984	0.4077		0.5219	False		,,,				2504	0.635					ENST00000426066.1																			0																																																			0							g.chr22:22663087A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663087A>G								NR_027293.1						0	526	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.303	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	42	0	0	0	1	0	4	42				
IRF8	3394	broad.mit.edu	37	16	85954816	85954816	+	Silent	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr16:85954816C>T	ENST00000268638.5	+	9	1631	c.1209C>T	c.(1207-1209)ttC>ttT	p.F403F	IRF8_ENST00000562492.1_Silent_p.F199F	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	403					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAGGTCTTCCGGATGTTTC	0.587																																						ENST00000268638.5																			0				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24						c.(1207-1209)ttC>ttT		interferon regulatory factor 8							60.0	66.0	64.0					16																	85954816		2198	4300	6498	SO:0001819	synonymous_variant	3394				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity	g.chr16:85954816C>T	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1209C>T	16.37:g.85954816C>T						IRF8_ENST00000562492.1_Silent_p.F199F	p.F403F	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN			9	1631	+		Prostate(104;0.0771)	403					A0AV82	Silent	SNP	ENST00000268638.5	37	c.1209C>T	CCDS10956.1																																																																																				0.587	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		6	113	0	0	0	1	0	6	113				
OR4C16	219428	broad.mit.edu	37	11	55339695	55339695	+	Missense_Mutation	SNP	G	G	A	rs374191202		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr11:55339695G>A	ENST00000314634.3	+	1	92	c.92G>A	c.(91-93)cGt>cAt	p.R31H		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R31H(2)|p.R31L(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				ATTTTTTTGCGTCTCTACTTG	0.368													g|||	1	0.000199681	0.0	0.0	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.001					ENST00000314634.3																			3	Substitution - Missense(3)	p.R31H(2)|p.R31L(1)	prostate(2)|lung(1)	central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41						c.(91-93)cGt>cAt		olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)							189.0	177.0	181.0					11																	55339695		2201	4296	6497	SO:0001583	missense	219428				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55339695G>A	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.92G>A	11.37:g.55339695G>A	ENSP00000324913:p.Arg31His						p.R31H	NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN			1	92	+		all_epithelial(135;0.0748)	31					Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	c.92G>A	CCDS31502.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.519004	0.27211	.	.	ENSG00000181935	ENST00000314634	T	0.00438	7.42	4.98	3.85	0.44370	.	2.239510	0.01631	N	0.023546	T	0.00300	0.0009	N	0.14661	0.345	0.09310	N	1	B	0.25351	0.124	B	0.12837	0.008	T	0.47156	-0.9139	10	0.87932	D	0	.	9.0123	0.36148	0.0:0.0:0.1863:0.8137	.	31	Q8NGL9	OR4CG_HUMAN	H	31	ENSP00000324913:R31H	ENSP00000324913:R31H	R	+	2	0	OR4C16	55096271	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.003000	0.12901	0.915000	0.36847	-0.425000	0.05940	CGT		0.368	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		59	110	0	0	0	1	0	59	110				
OCLN	100506658	broad.mit.edu	37	5	68849441	68849441	+	Missense_Mutation	SNP	G	G	C			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr5:68849441G>C	ENST00000355237.2	+	9	1948	c.1512G>C	c.(1510-1512)aaG>aaC	p.K504N	OCLN_ENST00000396442.2_Missense_Mutation_p.K504N|OCLN_ENST00000538151.1_Missense_Mutation_p.K253N|OCLN_ENST00000542132.1_Missense_Mutation_p.K182N|OCLN_ENST00000380766.2_Missense_Mutation_p.K450N|OCLN_ENST00000514370.1_3'UTR	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	504					apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AGCAGTTAAAGAGCAAATTGT	0.348																																						ENST00000355237.2																			0				endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6						c.(1510-1512)aaG>aaC		occludin							131.0	138.0	135.0					5																	68849441		2203	4298	6501	SO:0001583	missense	100506658				cellular component disassembly involved in apoptosis|protein complex assembly	integral to membrane|tight junction	protein binding|structural molecule activity	g.chr5:68849441G>C	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"""tight junction protein occludin TM4 minus"", ""phosphatase 1, regulatory subunit 115"""	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.1512G>C	5.37:g.68849441G>C	ENSP00000347379:p.Lys504Asn					OCLN_ENST00000538151.1_Missense_Mutation_p.K253N|OCLN_ENST00000396442.2_Missense_Mutation_p.K504N|OCLN_ENST00000380766.2_Missense_Mutation_p.K450N|OCLN_ENST00000542132.1_Missense_Mutation_p.K182N|OCLN_ENST00000514370.1_3'UTR	p.K504N	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)	9	1948	+		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)	504					B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	37	c.1512G>C	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.549059	0.65311	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766;ENST00000538151;ENST00000542132	T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78	5.6	4.54	0.55810	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.138190	0.64402	D	0.000008	T	0.52500	0.1738	M	0.79693	2.465	0.58432	D	0.999991	D	0.89917	1.0	D	0.83275	0.996	T	0.56721	-0.7932	10	0.66056	D	0.02	-2.827	14.371	0.66840	0.0857:0.0:0.9143:0.0	.	504	Q16625	OCLN_HUMAN	N	504;504;450;253;182	ENSP00000347379:K504N;ENSP00000379719:K504N;ENSP00000370143:K450N;ENSP00000445940:K253N;ENSP00000440000:K182N	ENSP00000347379:K504N	K	+	3	2	OCLN	68885197	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.649000	0.46656	2.653000	0.90120	0.552000	0.68991	AAG		0.348	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538		5	72	0	0	0	1	0	5	72				
GPR125	166647	broad.mit.edu	37	4	22390725	22390725	+	Silent	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:22390725C>T	ENST00000334304.5	-	18	2978	c.2709G>A	c.(2707-2709)cgG>cgA	p.R903R	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	903					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.R903R(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				GTGCGTTTGGCCGACTGCCGT	0.418																																						ENST00000334304.5																			1	Substitution - coding silent(1)	p.R903R(1)	lung(1)	breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56						c.(2707-2709)cgG>cgA		G protein-coupled receptor 125							206.0	217.0	213.0					4																	22390725		2203	4300	6503	SO:0001819	synonymous_variant	166647				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity	g.chr4:22390725C>T	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2709G>A	4.37:g.22390725C>T						GPR125_ENST00000282943.5_5'UTR	p.R903R	NM_145290.2	NP_660333.2	Q8IWK6	GP125_HUMAN			18	2978	-		Breast(46;0.198)	903					Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	37	c.2709G>A	CCDS33964.1																																																																																				0.418	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			5	384	0	0	0	1	0	5	384				
FRG1B	284802	broad.mit.edu	37	20	29628243	29628243	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr20:29628243T>C	ENST00000278882.3	+	6	625	c.245T>C	c.(244-246)tTg>tCg	p.L82S	FRG1B_ENST00000439954.2_Missense_Mutation_p.L87S|FRG1B_ENST00000358464.4_Missense_Mutation_p.L82S			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	82								p.L82S(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGGCTTTGTTGGCCTCAAAT	0.363																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.L82S(2)	urinary_tract(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(244-246)tTg>tCg																																						SO:0001583	missense	0							g.chr20:29628243T>C			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.245T>C	20.37:g.29628243T>C	ENSP00000278882:p.Leu82Ser					FRG1B_ENST00000439954.2_Missense_Mutation_p.L87S|FRG1B_ENST00000358464.4_Missense_Mutation_p.L82S	p.L82S							6	625	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.245T>C		.	.	.	.	.	.	.	.	.	.	t	12.14	1.848999	0.32699	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.49139	0.79	2.08	2.08	0.27032	Actin cross-linking (1);	0.147685	0.45361	D	0.000380	T	0.38665	0.1049	.	.	.	0.46185	D	0.99891	B;B	0.27656	0.03;0.184	B;B	0.35813	0.11;0.211	T	0.24548	-1.0157	9	0.38643	T	0.18	.	8.0833	0.30758	0.0:0.0:0.0:1.0	.	87;82	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	S	82;87;82	ENSP00000408863:L87S	ENSP00000278882:L82S	L	+	2	0	FRG1B	28241904	1.000000	0.71417	0.998000	0.56505	0.541000	0.35023	6.955000	0.76007	1.208000	0.43306	0.347000	0.21830	TTG		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	315	0	0	0	1	0	5	315				
ANKRD20A8P	729171	broad.mit.edu	37	2	95522786	95522786	+	RNA	SNP	T	T	C			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr2:95522786T>C	ENST00000432432.2	-	0	241					NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene									p.K44K(1)									CGGCGTCGCCTTTGACAGCTG	0.687																																						ENST00000432432.2																			1	Substitution - coding silent(1)	p.K44K(1)	prostate(1)																																																0							g.chr2:95522786T>C			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95522786T>C								NR_040113.1						0	241	-								A6NC18	RNA	SNP	ENST00000432432.2	37																																																																																						0.687	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene	OTTHUMT00000451404.1			3	81	0	0	0	1	0	3	81				
STPG2	285555	broad.mit.edu	37	4	98902451	98902451	+	Missense_Mutation	SNP	A	A	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr4:98902451A>T	ENST00000295268.3	-	6	720	c.631T>A	c.(631-633)Tca>Aca	p.S211T		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	211																	GGGGTGATTGATTTCATAGGT	0.363																																						ENST00000295268.3																			0											c.(631-633)Tca>Aca		sperm-tail PG-rich repeat containing 2							83.0	84.0	84.0					4																	98902451		2203	4300	6503	SO:0001583	missense	285555							g.chr4:98902451A>T	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.631T>A	4.37:g.98902451A>T	ENSP00000295268:p.Ser211Thr						p.S211T	NM_174952.2	NP_777612.1					6	720	-									Missense_Mutation	SNP	ENST00000295268.3	37	c.631T>A	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618232	0.46736	.	.	ENSG00000163116	ENST00000295268	T	0.12361	2.69	5.47	5.47	0.80525	.	0.192915	0.36591	N	0.002509	T	0.35248	0.0925	M	0.68317	2.08	0.31250	N	0.694152	D	0.76494	0.999	D	0.78314	0.991	T	0.36625	-0.9740	10	0.48119	T	0.1	-16.2935	14.5303	0.67920	1.0:0.0:0.0:0.0	.	211	Q8N412	CD037_HUMAN	T	211	ENSP00000295268:S211T	ENSP00000295268:S211T	S	-	1	0	C4orf37	99121474	1.000000	0.71417	0.951000	0.38953	0.697000	0.40408	5.813000	0.69201	2.061000	0.61500	0.460000	0.39030	TCA		0.363	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		34	88	0	0	0	1	0	34	88				
SNAP91	9892	broad.mit.edu	37	6	84366496	84366496	+	Missense_Mutation	SNP	T	T	C	rs372664943		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr6:84366496T>C	ENST00000439399.2	-	7	951	c.635A>G	c.(634-636)aAt>aGt	p.N212S	SNAP91_ENST00000437520.1_Missense_Mutation_p.N212S|SNAP91_ENST00000428679.2_Missense_Mutation_p.N212S|SNAP91_ENST00000369694.2_Missense_Mutation_p.N212S|SNAP91_ENST00000521743.1_Missense_Mutation_p.N212S|SNAP91_ENST00000520213.1_Missense_Mutation_p.N212S|SNAP91_ENST00000195649.6_Missense_Mutation_p.N212S|SNAP91_ENST00000520302.1_Missense_Mutation_p.N212S|SNAP91_ENST00000521485.1_Missense_Mutation_p.N212S	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	212					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AACACCATCATTGTAGCAAGC	0.383																																						ENST00000428679.2																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						c.(634-636)aAt>aGt		synaptosomal-associated protein, 91kDa		T	SER/ASN,SER/ASN,SER/ASN,SER/ASN	0,3790		0,0,1895	110.0	103.0	105.0		635,635,635,635	5.1	1.0	6		105	1,8237		0,1,4118	no	missense,missense,missense,missense	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	46,46,46,46	0,1,6013	CC,CT,TT		0.0121,0.0,0.0083	benign,benign,benign,benign	212/908,212/878,212/601,212/908	84366496	1,12027	1895	4119	6014	SO:0001583	missense	9892				clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding	g.chr6:84366496T>C	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.635A>G	6.37:g.84366496T>C	ENSP00000400459:p.Asn212Ser					SNAP91_ENST00000437520.1_Missense_Mutation_p.N212S|SNAP91_ENST00000521743.1_Missense_Mutation_p.N212S|SNAP91_ENST00000195649.6_Missense_Mutation_p.N212S|SNAP91_ENST00000521485.1_Missense_Mutation_p.N212S|SNAP91_ENST00000439399.2_Missense_Mutation_p.N212S|SNAP91_ENST00000520302.1_Missense_Mutation_p.N212S|SNAP91_ENST00000369694.2_Missense_Mutation_p.N212S|SNAP91_ENST00000520213.1_Missense_Mutation_p.N212S	p.N212S			O60641	AP180_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0967)	7	1228	-		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)	212					A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	37	c.635A>G	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.969094	0.74131	0.0	1.21E-4	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931	T;T;T;T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.11	5.11	0.69529	ANTH (1);Clathrin adaptor, phosphoinositide-binding, GAT-like (1);	0.000000	0.85682	D	0.000000	T	0.63129	0.2485	H	0.96662	3.86	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.999;0.997	D;D;D;D	0.74023	0.974;0.973;0.982;0.973	T	0.77768	-0.2464	10	0.87932	D	0	-13.6453	15.1975	0.73104	0.0:0.0:0.0:1.0	.	212;212;212;212	O60641-3;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	S	212	ENSP00000429776:N212S;ENSP00000358708:N212S;ENSP00000400459:N212S;ENSP00000195649:N212S;ENSP00000412492:N212S;ENSP00000413277:N212S;ENSP00000428511:N212S;ENSP00000428215:N212S;ENSP00000428026:N212S;ENSP00000430071:N212S	ENSP00000195649:N212S	N	-	2	0	SNAP91	84423215	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.997000	0.88414	2.056000	0.61249	0.383000	0.25322	AAT		0.383	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			3	22	0	0	0	1	0	3	22				
CCDC6	8030	broad.mit.edu	37	10	61564190	61564190	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr10:61564190G>A	ENST00000263102.6	-	7	1324	c.1093C>T	c.(1093-1095)Cct>Tct	p.P365S		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	365						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GGTGATATAGGCCTGCTTGAA	0.458			T	RET	NSCLC																																	ENST00000263102.6				Dom	yes		10	10q21	8030	T	coiled-coil domain containing 6			E	RET		NSCLC	CCDC6/RET(4)	0				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18						c.(1093-1095)Cct>Tct		coiled-coil domain containing 6							168.0	147.0	154.0					10																	61564190		2203	4300	6503	SO:0001583	missense	8030					cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton	g.chr10:61564190G>A	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1093C>T	10.37:g.61564190G>A	ENSP00000263102:p.Pro365Ser						p.P365S	NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN		Kidney(211;0.0597)	7	1324	-			365					Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	c.1093C>T	CCDS7257.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.779971	0.90195	.	.	ENSG00000108091	ENST00000263102	T	0.51817	0.69	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	L	0.49350	1.555	0.80722	D	1	D	0.63880	0.993	D	0.72982	0.979	T	0.54077	-0.8347	10	0.18710	T	0.47	-11.4197	19.3389	0.94334	0.0:0.0:1.0:0.0	.	365	Q16204	CCDC6_HUMAN	S	365	ENSP00000263102:P365S	ENSP00000263102:P365S	P	-	1	0	CCDC6	61234196	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.859000	0.99545	2.593000	0.87608	0.655000	0.94253	CCT		0.458	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436		32	68	0	0	0	1	0	32	68				
PARP16	54956	broad.mit.edu	37	15	65563325	65563325	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr15:65563325C>T	ENST00000261888.6	-	2	705	c.260G>A	c.(259-261)aGc>aAc	p.S87N	PARP16_ENST00000558873.1_5'UTR|PARP16_ENST00000444347.2_Intron	NM_017851.4	NP_060321.3	Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	87	PARP alpha-helical.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						TAAAATCCAGCTCACCAGGTC	0.532																																					NSCLC(50;885 1163 13509 21242 41978)	ENST00000261888.6																			0				kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						c.(259-261)aGc>aAc		poly (ADP-ribose) polymerase family, member 16							202.0	198.0	199.0					15																	65563325		2201	4299	6500	SO:0001583	missense	54956					integral to membrane	NAD+ ADP-ribosyltransferase activity	g.chr15:65563325C>T	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"""Poly (ADP-ribose) polymerases"""	26040	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 30"""	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000261888.6:c.260G>A	15.37:g.65563325C>T	ENSP00000261888:p.Ser87Asn					PARP16_ENST00000558873.1_5'UTR|PARP16_ENST00000444347.2_Intron	p.S87N	NM_017851.4	NP_060321.3	Q8N5Y8	PAR16_HUMAN			2	705	-			87			PARP catalytic.		Q6PK64|Q9NX03	Missense_Mutation	SNP	ENST00000261888.6	37	c.260G>A	CCDS10204.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616169	0.46631	.	.	ENSG00000138617	ENST00000261888	T	0.43688	0.94	5.8	4.89	0.63831	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.265975	0.49916	N	0.000134	T	0.32102	0.0818	L	0.34521	1.04	0.80722	D	1	P;P	0.37781	0.608;0.473	B;B	0.36719	0.231;0.116	T	0.05484	-1.0882	10	0.20519	T	0.43	-13.4614	14.0809	0.64922	0.0:0.928:0.0:0.072	.	87;87	Q8N5Y8-3;Q8N5Y8	.;PAR16_HUMAN	N	87	ENSP00000261888:S87N	ENSP00000261888:S87N	S	-	2	0	PARP16	63350378	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.395000	0.52558	1.461000	0.47929	0.655000	0.94253	AGC		0.532	PARP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256827.2	NM_017851		5	445	0	0	0	1	0	5	445				
ABCC3	8714	broad.mit.edu	37	17	48755185	48755185	+	Silent	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:48755185G>A	ENST00000285238.8	+	24	3539	c.3459G>A	c.(3457-3459)gaG>gaA	p.E1153E		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1153	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	ACTTTTCGGAGACAGTGACTG	0.547																																						ENST00000285238.8																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33						c.(3457-3459)gaG>gaA		ATP-binding cassette, sub-family C (CFTR/MRP), member 3	Glibenclamide(DB01016)						134.0	137.0	136.0					17																	48755185		2203	4300	6503	SO:0001819	synonymous_variant	8714				bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity	g.chr17:48755185G>A	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3459G>A	17.37:g.48755185G>A							p.E1153E	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		24	3539	+			1153			ABC transmembrane type-1 2.		B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	c.3459G>A	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	9.184	1.024416	0.19433	.	.	ENSG00000108846	ENST00000513745	.	.	.	5.7	4.73	0.59995	.	.	.	.	.	T	0.62744	0.2453	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61158	-0.7119	4	.	.	.	-34.7031	11.3055	0.49332	0.1914:0.0:0.8086:0.0	.	.	.	.	N	257	.	.	D	+	1	0	ABCC3	46110184	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.185000	0.50934	1.409000	0.46915	0.655000	0.94253	GAC		0.547	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		6	315	0	0	0	1	0	6	315				
STAG1	10274	broad.mit.edu	37	3	136240172	136240172	+	Nonsense_Mutation	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr3:136240172G>A	ENST00000383202.2	-	7	815	c.559C>T	c.(559-561)Cga>Tga	p.R187*	STAG1_ENST00000434713.2_5'UTR|STAG1_ENST00000236698.5_Nonsense_Mutation_p.R187*|STAG1_ENST00000480733.1_Nonsense_Mutation_p.R187*	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	187					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R187*(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TGACACTGTCGAATCAGGACT	0.398																																						ENST00000383202.2																			1	Substitution - Nonsense(1)	p.R187*(1)	large_intestine(1)	NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(559-561)Cga>Tga		stromal antigen 1							103.0	99.0	100.0					3																	136240172		2203	4300	6503	SO:0001587	stop_gained	10274				cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chr3:136240172G>A	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.559C>T	3.37:g.136240172G>A	ENSP00000372689:p.Arg187*					STAG1_ENST00000236698.5_Nonsense_Mutation_p.R187*|STAG1_ENST00000480733.1_Nonsense_Mutation_p.R187*|STAG1_ENST00000434713.2_5'UTR	p.R187*	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN			7	815	-			187					O00539|Q6P275	Nonsense_Mutation	SNP	ENST00000383202.2	37	c.559C>T	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	G	38	6.682511	0.97759	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000480733	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0024	0.97423	0.0:0.0:1.0:0.0	.	.	.	.	X	187	.	ENSP00000236698:R187X	R	-	1	2	STAG1	137722862	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.722000	0.93159	0.467000	0.42956	CGA		0.398	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		4	196	0	0	0	1	0	4	196				
ITGB4	3691	broad.mit.edu	37	17	73725516	73725516	+	Splice_Site	SNP	C	C	T			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:73725516C>T	ENST00000200181.3	+	7	924	c.737C>T	c.(736-738)aCg>aTg	p.T246M	ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000579662.1_Splice_Site_p.T246M|ITGB4_ENST00000449880.2_Splice_Site_p.T246M|ITGB4_ENST00000339591.3_Splice_Site_p.T246M|ITGB4_ENST00000450894.3_Splice_Site_p.T246M	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	246	VWFA.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCTGTGTGCACGGTGGGCACT	0.637																																						ENST00000200181.3																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43						c.e7+1		integrin, beta 4							51.0	48.0	49.0					17																	73725516		2203	4300	6503	SO:0001630	splice_region_variant	3691				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	g.chr17:73725516C>T		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.738+1C>T	17.37:g.73725516C>T						ITGB4_ENST00000450894.3_Splice_Site_p.T246_splice|ITGB4_ENST00000449880.2_Splice_Site_p.T246_splice|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000339591.3_Splice_Site_p.T246_splice|ITGB4_ENST00000579662.1_Splice_Site_p.T246_splice	p.T246_splice	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		7	924	+	all_cancers(13;1.5e-07)		246			VWFA.		A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Splice_Site	SNP	ENST00000200181.3	37	c.738_splice	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388559	0.25118	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.92805	-3.11;-3.11;-3.11	5.66	4.64	0.57946	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.286939	0.34750	N	0.003708	D	0.95274	0.8467	M	0.79123	2.44	0.38499	D	0.94817	D;D;D;D	0.89917	0.999;0.998;0.999;1.0	P;P;D;D	0.69479	0.894;0.884;0.93;0.964	D	0.95424	0.8510	10	0.49607	T	0.09	.	13.9078	0.63848	0.2255:0.7745:0.0:0.0	.	246;246;246;246	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	M	162;246;246;246	ENSP00000200181:T246M;ENSP00000344079:T246M;ENSP00000400217:T246M	ENSP00000200181:T246M	T	+	2	0	ITGB4	71237111	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	1.816000	0.38992	2.668000	0.90789	0.655000	0.94253	ACG		0.637	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		Missense_Mutation	8	18	0	0	0	1	0	8	18				
PRG4	10216	broad.mit.edu	37	1	186276640	186276640	+	Missense_Mutation	SNP	A	A	C			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr1:186276640A>C	ENST00000445192.2	+	7	1834	c.1789A>C	c.(1789-1791)Acc>Ccc	p.T597P	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.T556P|PRG4_ENST00000367486.3_Missense_Mutation_p.T554P|PRG4_ENST00000367485.4_Missense_Mutation_p.T504P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	597	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.T597P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACCCACCACCACCAAGAAGCC	0.652																																						ENST00000445192.2																			1	Substitution - Missense(1)	p.T597P(1)	prostate(1)	NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						c.(1789-1791)Acc>Ccc		proteoglycan 4							87.0	83.0	85.0					1																	186276640		2203	4300	6503	SO:0001583	missense	10216				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity	g.chr1:186276640A>C	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1789A>C	1.37:g.186276640A>C	ENSP00000399679:p.Thr597Pro					PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.T556P|PRG4_ENST00000367486.3_Missense_Mutation_p.T554P|PRG4_ENST00000367485.4_Missense_Mutation_p.T504P	p.T597P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN			7	1834	+			597			59 X 8 AA repeats of K-X-P-X-P-T-T-X.		Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	c.1789A>C	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	1.907	-0.451678	0.04572	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.04360	3.64;3.75;3.64;3.73	2.4	-2.78	0.05859	.	0.762931	0.10621	N	0.653340	T	0.01189	0.0039	N	0.00465	-1.465	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47736	-0.9094	9	.	.	.	.	7.4224	0.27079	0.6922:0.2055:0.0:0.1023	.	463;504;597;556	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	P	554;463;556;504;597	ENSP00000356456:T554P;ENSP00000356453:T556P;ENSP00000356455:T504P;ENSP00000399679:T597P	.	T	+	1	0	PRG4	184543263	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.955000	0.00675	-1.097000	0.03042	-4.201000	0.00009	ACC		0.652	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		6	81	0	0	0	1	0	6	81				
LYST	1130	broad.mit.edu	37	1	235929502	235929502	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr1:235929502G>A	ENST00000389794.3	-	21	6172	c.5998C>T	c.(5998-6000)Ctt>Ttt	p.L2000F	LYST_ENST00000389793.2_Missense_Mutation_p.L2000F|LYST_ENST00000536965.1_3'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2000					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GGAGATCCAAGGACTTCTGCT	0.378																																						ENST00000389794.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162						c.(5998-6000)Ctt>Ttt		lysosomal trafficking regulator							156.0	171.0	166.0					1																	235929502		2203	4300	6503	SO:0001583	missense	1130				defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding	g.chr1:235929502G>A	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.5998C>T	1.37:g.235929502G>A	ENSP00000374444:p.Leu2000Phe					LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.L2000F	p.L2000F			Q99698	LYST_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.000674)		21	6172	-	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	2000					O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	c.5998C>T	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544056	0.86022	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.65364	-0.15;-0.15	5.36	5.36	0.76844	.	0.220699	0.42053	D	0.000779	T	0.78477	0.4289	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	T	0.79852	-0.1628	10	0.72032	D	0.01	.	19.4366	0.94798	0.0:0.0:1.0:0.0	.	2000	Q99698	LYST_HUMAN	F	2000	ENSP00000374444:L2000F;ENSP00000374443:L2000F	ENSP00000374443:L2000F	L	-	1	0	LYST	233996125	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.334000	0.79224	2.669000	0.90835	0.585000	0.79938	CTT		0.378	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			111	236	0	0	0	1	0	111	236				
DLC1	10395	broad.mit.edu	37	8	13357011	13357011	+	Silent	SNP	G	G	A			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr8:13357011G>A	ENST00000276297.4	-	2	979	c.570C>T	c.(568-570)agC>agT	p.S190S	DLC1_ENST00000316609.5_Silent_p.S190S|DLC1_ENST00000511869.1_Silent_p.S190S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	190					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AAAGCTCCAGGCTTTTACTTA	0.383																																						ENST00000276297.4																			0				NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						c.(568-570)agC>agT		deleted in liver cancer 1							120.0	124.0	123.0					8																	13357011		2203	4300	6503	SO:0001819	synonymous_variant	10395				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding	g.chr8:13357011G>A	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.570C>T	8.37:g.13357011G>A						DLC1_ENST00000316609.5_Silent_p.S190S|DLC1_ENST00000511869.1_Silent_p.S190S	p.S190S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN			2	979	-			190					B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	c.570C>T	CCDS5989.1																																																																																				0.383	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		7	281	0	0	0	1	0	7	281				
SLC7A1	6541	broad.mit.edu	37	13	30091751	30091751	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr13:30091751T>C	ENST00000380752.5	-	10	1855	c.1469A>G	c.(1468-1470)aAa>aGa	p.K490R	SLC7A1_ENST00000473577.1_5'UTR	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	490					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CCCAGAGATTTTGGAAGGCTC	0.473																																						ENST00000380752.5																			0				endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24						c.(1468-1470)aAa>aGa		solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)						167.0	165.0	166.0					13																	30091751		2203	4300	6503	SO:0001583	missense	6541				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity	g.chr13:30091751T>C	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"""Solute carriers"""	11057	protein-coding gene	gene with protein product	"""ecotropic retroviral receptor"", ""amino acid transporter, cationic 1"""	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.1469A>G	13.37:g.30091751T>C	ENSP00000370128:p.Lys490Arg					SLC7A1_ENST00000473577.1_5'UTR	p.K490R	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	10	1855	-		Lung SC(185;0.0257)|Breast(139;0.238)	490					Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	37	c.1469A>G	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	T	6.343	0.431411	0.12045	.	.	ENSG00000139514	ENST00000380752	D	0.85955	-2.05	5.13	3.95	0.45737	.	0.614674	0.17151	N	0.185049	T	0.72020	0.3409	L	0.28274	0.84	0.29737	N	0.837388	B	0.02656	0.0	B	0.04013	0.001	T	0.58216	-0.7675	10	0.10377	T	0.69	.	7.6847	0.28534	0.0:0.1637:0.0:0.8363	.	490	P30825	CTR1_HUMAN	R	490	ENSP00000370128:K490R	ENSP00000370128:K490R	K	-	2	0	SLC7A1	28989751	0.801000	0.28930	0.878000	0.34440	0.558000	0.35554	0.518000	0.22847	0.924000	0.37069	0.533000	0.62120	AAA		0.473	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		90	86	0	0	0	1	0	90	86				
RP11-423O2.5	0	broad.mit.edu	37	1	142803276	142803278	+	lincRNA	DEL	AAC	AAC	-	rs140309984|rs145869340		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr1:142803276_142803278delAAC	ENST00000423385.1	-	0	1687_1689																											ACCAAACCAAaacaacaacaaca	0.345																																						ENST00000423385.1																			0																																																			0							g.chr1:142803276_142803278delAAC																													1.37:g.142803285_142803287delAAC														0	1687_1689	-									RNA	DEL	ENST00000423385.1	37																																																																																						0.345	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			5	5						5	5	---	---	---	---
MCC	4163	broad.mit.edu	37	5	112824048	112824049	+	In_Frame_Ins	INS	-	-	GCC	rs35336557|rs531679771|rs370593160	byFrequency	TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr5:112824048_112824049insGCC	ENST00000408903.3	-	1	478_479	c.63_64insGGC	c.(61-66)ggcagc>ggcGGCagc	p.21_22insG		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctgctgccgctgccgccgccgc	0.738														1663	0.332069	0.0227	0.3487	5008	,	,		8489	0.5208		0.3668	False		,,,				2504	0.5082					ENST00000408903.3																			0				endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(61-66)gggcgg>ggGGCgcgg		mutated in colorectal cancers																																				SO:0001652	inframe_insertion	4163				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity	g.chr5:112824048_112824049insGCC		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.61_63dupGGC	5.37:g.112824055_112824057dupGCC	ENSP00000386227:p.Gly22_Gly23dup						p.21_22GR>GAR	NM_001085377.1	NP_001078846.1	P23508	CRCM_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)	1	478_479	-		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)	549					D3DT05|Q6ZR04	In_Frame_Ins	INS	ENST00000408903.3	37	c.63_64insGGC	CCDS43351.1																																																																																				0.738	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377		14	16						14	16	---	---	---	---
TOX4	9878	broad.mit.edu	37	14	21961060	21961062	+	In_Frame_Del	DEL	GCT	GCT	-	rs571846793		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr14:21961060_21961062delGCT	ENST00000405508.1	+	8	1561_1563	c.1285_1287delGCT	c.(1285-1287)gctdel	p.A434del	TOX4_ENST00000448790.2_In_Frame_Del_p.A411del|TOX4_ENST00000262709.3_In_Frame_Del_p.A434del			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	434	Gln/Pro-rich.|Poly-Ala.					chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)	p.A429A(1)		large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		GGCAGCAGCAGCTGCTGCTGCTG	0.581																																						ENST00000405508.1																			1	Substitution - coding silent(1)	p.A429A(1)	large_intestine(1)	large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						c.(1285-1287)del		TOX high mobility group box family member 4																																				SO:0001651	inframe_deletion	9878					chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding	g.chr14:21961060_21961062delGCT	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.1285_1287delGCT	14.37:g.21961069_21961071delGCT	ENSP00000385102:p.Ala434del					TOX4_ENST00000448790.2_In_Frame_Del_p.A411del|TOX4_ENST00000262709.3_In_Frame_Del_p.A434del	p.A434del			O94842	TOX4_HUMAN	Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)	8	1561_1563	+	all_cancers(95;0.000465)		434			Gln/Pro-rich.|Poly-Ala.		B4DPY8|B4DSM0|E7EV69	In_Frame_Del	DEL	ENST00000405508.1	37	c.1285_1287delGCT	CCDS32043.1																																																																																				0.581	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828		7	285						7	285	---	---	---	---
MED9	55090	broad.mit.edu	37	17	17394705	17394707	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:17394705_17394707delCAG	ENST00000268711.3	+	2	393_395	c.337_339delCAG	c.(337-339)cagdel	p.Q117del		NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN	mediator complex subunit 9	117						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						GAGCCCCGAACAGCAGCAGCAGC	0.581																																						ENST00000268711.3																			0				cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						c.(337-339)del		mediator complex subunit 9																																				SO:0001651	inframe_deletion	55090				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		protein binding	g.chr17:17394705_17394707delCAG	BC000647	CCDS11184.1	17p11.2	2007-07-30	2007-07-30		ENSG00000141026	ENSG00000141026			25487	protein-coding gene	gene with protein product		609878	"""mediator of RNA polymerase II transcription, subunit 9 homolog (S. cerevisiae)"""			11997338	Standard	NM_018019		Approved	FLJ10193, MED25	uc002grh.1	Q9NWA0	OTTHUMG00000059293	ENST00000268711.3:c.337_339delCAG	17.37:g.17394714_17394716delCAG	ENSP00000268711:p.Gln117del						p.Q117del	NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN			2	393_395	+			117						In_Frame_Del	DEL	ENST00000268711.3	37	c.337_339delCAG	CCDS11184.1																																																																																				0.581	MED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131669.2	NM_018019		7	196						7	196	---	---	---	---
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr17:45219612delA	ENST00000066544.3	-	11	1454	c.1361delT	c.(1360-1362)ctafs	p.L454fs	CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGCTTTTTGTAGATTAAAGGC	0.308																																						ENST00000066544.3																			0				NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						c.(1360-1362)cafs		cell division cycle 27							30.0	30.0	30.0					17																	45219612		2201	4295	6496	SO:0001589	frameshift_variant	996				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding	g.chr17:45219612delA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1361delT	17.37:g.45219612delA	ENSP00000066544:p.Leu454fs					CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs	p.L454fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN			11	1454	-			454					G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	37	c.1361delT	CCDS11509.1																																																																																				0.308	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			9	74						9	74	---	---	---	---
PSG7	5676	broad.mit.edu	37	19	43440068	43440069	+	RNA	DEL	AC	AC	-	rs147024666		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr19:43440068_43440069delAC	ENST00000406070.2	-	0	161				PSG7_ENST00000471557.1_RNA|PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				acacacacaaacacacacacac	0.495																																						ENST00000446844.3																			0													pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)																																						5676				female pregnancy	extracellular region		g.chr19:43440068_43440069delAC			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43440078_43440079delAC						PSG7_ENST00000406070.2_RNA				Q13046	PSG7_HUMAN			0	154	-		Prostate(69;0.00682)						Q15232	RNA	DEL	ENST00000406070.2	37																																																																																						0.495	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650		7	12						7	12	---	---	---	---
ANKRD20A18P	391269	broad.mit.edu	37	21	15436915	15436915	+	RNA	DEL	G	G	-	rs148280092		TCGA-QH-A6CY-01A-11D-A32B-08	TCGA-QH-A6CY-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e810c032-3bcd-4baf-9e72-58ef00fb0ac7	27e7dbae-bfb7-4634-98cd-9f4211d864d6	g.chr21:15436915delG	ENST00000428809.1	+	0	177				AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000448463.1_RNA																							CCCCTGGGACGGGGGCCTTGG	0.687																																						ENST00000428809.1																			0																																																			0							g.chr21:15436915delG																													21.37:g.15436915delG														0	177	+									RNA	DEL	ENST00000428809.1	37																																																																																						0.687	AP001347.6-001	KNOWN	basic	antisense	antisense	OTTHUMT00000157812.1			4	7						4	7	---	---	---	---
