#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
APOBR	55911	hgsc.bcm.edu	37	16	28507398	28507424	+	Splice_Site	DEL	GGGACAGCCTCAGGAGGGGAGGAGGCC	GGGACAGCCTCAGGAGGGGAGGAGGCC	-	rs148114931|rs365499|rs62034314|rs62034315|rs441214	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GGGACAGCCTCAGGAGGGGAGGAGGCC	GGGACAGCCTCAGGAGGGGAGGAGGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr16:28507398_28507424delGGGACAGCCTCAGGAGGGGAGGAGGCC	ENST00000431282.1	+	2	1046_1058	c.1036_1048delGGGACAGCCTCAGGAGGGGAGGAGGCC	c.(1036-1050)gggacagcctcagga>ga	p.GTASG346del	APOBR_ENST00000564831.1_In_Frame_Del_p.GTASGGEEA355del|APOBR_ENST00000328423.5_Splice_Site_p.GTASG346del|CLN3_ENST00000569430.1_5'Flank|CLN3_ENST00000567160.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	346	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						CGGGGAGGCTGGGACAGCCTCAGGAGGGGAGGAGGCCGGGACAGCCT	0.705																																																	0										815,1911		288,239,836						-6.7	0.0		dbSNP_107	12	1986,4414		639,708,1853	no	coding-near-splice	APOBR	NM_018690.3		927,947,2689	A1A1,A1R,RR		31.0312,29.8973,30.6925				2801,6325				SO:0001630	splice_region_variant	0			AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1048+1GGGACAGCCTCAGGAGGGGAGGAGGCC>-	16.37:g.28507398_28507424delGGGACAGCCTCAGGAGGGGAGGAGGCC		Somatic		WXS	Illumina HiSeq	Phase_I	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Frame_Shift_Del	DEL	ENST00000431282.1	37																																																																																					0.705	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_182804	In_Frame_Del
AUTS2	26053	broad.mit.edu	37	7	70255256	70255256	+	Silent	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr7:70255256C>T	ENST00000342771.4	+	19	3375	c.3054C>T	c.(3052-3054)ccC>ccT	p.P1018P	AUTS2_ENST00000406775.2_Silent_p.P994P	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1018								p.P1018P(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ACCCGGGGCCCCTGGCCTCGA	0.677																																																	1	Substitution - coding silent(1)	kidney(1)											22.0	25.0	24.0					7																	70255256		2183	4247	6430	SO:0001819	synonymous_variant	26053			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3054C>T	7.37:g.70255256C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1																																																																																				0.677	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			
C1orf116	79098	broad.mit.edu;ucsc.edu	37	1	207200938	207200938	+	Silent	SNP	G	G	C	rs551306826		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:207200938G>C	ENST00000359470.5	-	2	255	c.6C>G	c.(4-6)ccC>ccG	p.P2P	C1orf116_ENST00000461135.2_Intron	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	2						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.P2P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					GCTCCCTCTCGGGCATCACCC	0.612																																																	1	Substitution - coding silent(1)	kidney(1)											55.0	52.0	53.0					1																	207200938		2203	4300	6503	SO:0001819	synonymous_variant	79098				CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"""specifically androgen-regulated gene"""	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.6C>G	1.37:g.207200938G>C		Somatic		WXS	Illumina GAIIx	Phase_I	C9JV41|Q658X3	Silent	SNP	ENST00000359470.5	37	CCDS1475.1																																																																																				0.612	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1		NM_024115	
C6orf132	647024	hgsc.bcm.edu	37	6	42075105	42075131	+	In_Frame_Del	DEL	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT	-	rs553334748|rs539692316	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENST00000341865.4	-	4	518_544	c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	c.(517-546)ccacctcccctgctgctggaacccccaccc>ccc	p.173_182PPPLLLEPPP>P		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	173	Pro-rich.									breast(1)	1						gctgggcgggggtgggggttccagcagcaggggaggtggtgggggtg	0.665																																																	0										8,1312		4,0,656						1.1	0.5			2	76,2832		27,22,1405	no	coding	C6orf132	NM_001164446.1		31,22,2061	A1A1,A1R,RR		2.6135,0.6061,1.9868				84,4144				SO:0001651	inframe_deletion	647024				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	6.37:g.42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENSP00000341368:p.Pro173_Pro181del	Somatic		WXS	Illumina HiSeq	Phase_I	A6NI05	In_Frame_Del	DEL	ENST00000341865.4	37	CCDS47428.1																																																																																				0.665	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2		NM_001164446	
CACNA1B	774	broad.mit.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559|rs11137342|rs370787788|rs551405755	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr9:140918171_140918185delGGAGAAGGAGACCAC	ENST00000371372.1	+	19	3121_3135	c.2976_2990delGGAGAAGGAGACCAC	c.(2974-2991)gtggagaaggagaccacg>gtg	p.EKETT993del	CACNA1B_ENST00000277551.2_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000277549.5_In_Frame_Del_p.EKETT185del|CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371363.1_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000371355.4_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371357.1_In_Frame_Del_p.EKETT994del	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	993					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGAGGCTGTGGAGAAGGAGACCACGGAGAAGGAG	0.735														1990	0.397364	0.6225	0.1282	5008	,	,		9031	0.6349		0.1521	False		,,,				2504	0.2914																1	Deletion - In frame(1)	breast(1)								1091,1197		364,363,417						-1.3	0.0		dbSNP_134	8	691,4399		126,439,1980	no	coding	CACNA1B	NM_000718.3		490,802,2397	A1A1,A1R,RR		13.5756,47.6836,24.1529				1782,5596				SO:0001651	inframe_deletion	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2976_2990delGGAGAAGGAGACCAC	9.37:g.140918171_140918185delGGAGAAGGAGACCAC	ENSP00000360423:p.Glu993_Thr997del	Somatic		WXS	Illumina GAIIx	Phase_I	B1AQK5	In_Frame_Del	DEL	ENST00000371372.1	37	CCDS59522.1																																																																																				0.735	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1		NM_000718	
CACNA2D1	781	broad.mit.edu	37	7	81598283	81598283	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr7:81598283C>T	ENST00000356253.5	-	29	2606	c.2351G>A	c.(2350-2352)gGa>gAa	p.G784E	CACNA2D1_ENST00000535308.1_Intron|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.G772E			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	784					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G772E(2)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GGCACCAGGTCCACTTTCtaa	0.284																																																	2	Substitution - Missense(2)	ovary(1)|kidney(1)											73.0	78.0	76.0					7																	81598283		2203	4295	6498	SO:0001583	missense	781			M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2351G>A	7.37:g.81598283C>T	ENSP00000348589:p.Gly784Glu	Somatic		WXS	Illumina GAIIx	Phase_I	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	C	13.48	2.249383	0.39797	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.68903	-0.36;-0.36	5.07	5.07	0.68467	.	0.333148	0.34580	N	0.003860	T	0.53802	0.1819	L	0.31065	0.9	0.80722	D	1	B	0.31383	0.321	B	0.31946	0.138	T	0.50233	-0.8852	10	0.12430	T	0.62	-18.191	15.9532	0.79859	0.0:1.0:0.0:0.0	.	772	P54289-2	.	E	772;791;784	ENSP00000349320:G772E;ENSP00000348589:G784E	ENSP00000284088:G791E	G	-	2	0	CACNA2D1	81436219	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.662000	0.54510	2.518000	0.84900	0.484000	0.47621	GGA		0.284	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				
CD28	940	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	204591400	204591400	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:204591400G>A	ENST00000324106.8	+	2	246	c.97G>A	c.(97-99)Gac>Aac	p.D33N	CD28_ENST00000374478.4_Intron|CD28_ENST00000458610.2_Missense_Mutation_p.D47N|CD28_ENST00000374481.3_Missense_Mutation_p.D33N	NM_001243077.1|NM_006139.3	NP_001230006.1|NP_006130.1	P10747	CD28_HUMAN	CD28 molecule	33	Ig-like V-type.				apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cytokine biosynthetic process (GO:0042089)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|negative thymic T cell selection (GO:0045060)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of inflammatory response to antigenic stimulus (GO:0002863)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of mitosis (GO:0045840)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of viral genome replication (GO:0045070)|regulation of defense response to virus by virus (GO:0050690)|regulatory T cell differentiation (GO:0045066)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|SH3/SH2 adaptor activity (GO:0005070)	p.D33N(2)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13						TGTAGCGTACGACAATGCGGT	0.433																																																	2	Substitution - Missense(2)	kidney(1)|endometrium(1)											103.0	96.0	98.0					2																	204591400		2203	4300	6503	SO:0001583	missense	940			J02988	CCDS2361.1, CCDS58749.1	2q33	2013-01-11	2006-03-28		ENSG00000178562	ENSG00000178562		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1653	protein-coding gene	gene with protein product	"""T-cell-specific surface glycoprotein"""	186760	"""CD28 antigen (Tp44)"""			1355979	Standard	NM_006139		Approved		uc002vah.4	P10747	OTTHUMG00000132878	ENST00000324106.8:c.97G>A	2.37:g.204591400G>A	ENSP00000324890:p.Asp33Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAC1|Q13964|Q52M23|Q70WG0|Q8NI54|Q8NI55|Q8NI56|Q8WXJ2|Q9BYV0	Missense_Mutation	SNP	ENST00000324106.8	37	CCDS2361.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.896542	0.00522	.	.	ENSG00000178562	ENST00000374481;ENST00000458610;ENST00000324106	T;T;T	0.79352	-1.26;-0.21;-0.21	5.62	-2.53	0.06326	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.551144	0.19608	N	0.110215	T	0.42359	0.1199	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44772	-0.9306	10	0.02654	T	1	-16.2168	6.4438	0.21865	0.4967:0.1316:0.3718:0.0	.	33	P10747	CD28_HUMAN	N	33;47;33	ENSP00000363605:D33N;ENSP00000393648:D47N;ENSP00000324890:D33N	ENSP00000324890:D33N	D	+	1	0	CD28	204299645	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.040000	0.12104	-0.732000	0.04856	-1.080000	0.02220	GAC		0.433	CD28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256366.3		NM_006139	
COG5	10466	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	106888896	106888896	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr7:106888896C>T	ENST00000347053.3	-	16	1878	c.1828G>A	c.(1828-1830)Gtg>Atg	p.V610M	COG5_ENST00000393603.2_Missense_Mutation_p.V631M|COG5_ENST00000297135.3_Missense_Mutation_p.V631M	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	610					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.V631M(1)		breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GCATCTCCCACAGAAGTGAGT	0.333																																																	1	Substitution - Missense(1)	kidney(1)											127.0	122.0	124.0					7																	106888896		2203	4300	6503	SO:0001583	missense	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1828G>A	7.37:g.106888896C>T	ENSP00000334703:p.Val610Met	Somatic		WXS	Illumina HiSeq	Phase_I	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429695	0.62844	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.59502	0.26;0.26;0.26	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.59238	0.2179	L	0.43152	1.355	0.80722	D	1	P;P	0.48764	0.915;0.82	P;B	0.46510	0.519;0.446	T	0.57306	-0.7834	10	0.41790	T	0.15	-13.3454	19.7325	0.96188	0.0:1.0:0.0:0.0	.	610;631	Q9UP83;Q9UP83-2	COG5_HUMAN;.	M	610;631;631	ENSP00000334703:V610M;ENSP00000297135:V631M;ENSP00000377228:V631M	ENSP00000297135:V631M	V	-	1	0	COG5	106676132	1.000000	0.71417	0.964000	0.40570	0.958000	0.62258	6.637000	0.74304	2.763000	0.94921	0.563000	0.77884	GTG		0.333	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			
DDI1	414301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	103908556	103908556	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:103908556C>T	ENST00000302259.3	+	1	1249	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	336							aspartic-type endopeptidase activity (GO:0004190)	p.R336W(2)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AGATATGCTCCGGAGACATCA	0.443																																																	2	Substitution - Missense(2)	kidney(2)											131.0	124.0	126.0					11																	103908556		2202	4299	6501	SO:0001583	missense	414301				CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.1006C>T	11.37:g.103908556C>T	ENSP00000302805:p.Arg336Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.451721	0.43531	.	.	ENSG00000170967	ENST00000302259	T	0.51817	0.69	5.21	2.88	0.33553	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.101165	0.64402	D	0.000003	T	0.61986	0.2391	M	0.68317	2.08	0.43603	D	0.995963	D	0.76494	0.999	D	0.65573	0.936	T	0.63287	-0.6671	10	0.87932	D	0	-22.0794	10.8597	0.46819	0.6824:0.3176:0.0:0.0	.	336	Q8WTU0	DDI1_HUMAN	W	336	ENSP00000302805:R336W	ENSP00000302805:R336W	R	+	1	2	DDI1	103413766	1.000000	0.71417	0.989000	0.46669	0.138000	0.21146	4.376000	0.59556	0.522000	0.28464	-0.262000	0.10625	CGG		0.443	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1		NM_001001711	
DEFB115	245929	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	29847316	29847316	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr20:29847316A>G	ENST00000400552.1	+	2	148	c.148A>G	c.(148-150)Aaa>Gaa	p.K50E		NM_001037730.1	NP_001032819.1	Q30KQ5	DB115_HUMAN	defensin, beta 115	50					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.K50E(1)		kidney(1)|lung(3)|ovary(1)|skin(1)	6			Colorectal(19;0.00445)|COAD - Colon adenocarcinoma(19;0.0347)			GAAATCATGCAAAGAAATTGA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											83.0	79.0	80.0					20																	29847316		1834	4090	5924	SO:0001583	missense	245929			DQ012019	CCDS42859.1	20q11.1	2008-07-17			ENSG00000215547	ENSG00000215547		"""Defensins, beta"""	18096	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037730		Approved	DEFB-15	uc002wvp.1	Q30KQ5	OTTHUMG00000159284	ENST00000400552.1:c.148A>G	20.37:g.29847316A>G	ENSP00000383398:p.Lys50Glu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000400552.1	37	CCDS42859.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.940854	0.34283	.	.	ENSG00000215547	ENST00000400552	T	0.33438	1.41	2.94	2.94	0.34122	.	.	.	.	.	T	0.41305	0.1153	.	.	.	0.09310	N	1	D	0.60160	0.987	P	0.56088	0.791	T	0.14062	-1.0486	8	0.59425	D	0.04	.	7.7125	0.28686	1.0:0.0:0.0:0.0	.	50	Q30KQ5	DB115_HUMAN	E	50	ENSP00000383398:K50E	ENSP00000383398:K50E	K	+	1	0	DEFB115	29310977	0.640000	0.27243	0.296000	0.24974	0.315000	0.28087	1.219000	0.32479	1.612000	0.50221	0.329000	0.21502	AAA		0.338	DEFB115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354402.1		NM_001037730	
DHX8	1659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	41582097	41582097	+	Silent	SNP	G	G	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr17:41582097G>T	ENST00000262415.3	+	12	1704	c.1632G>T	c.(1630-1632)ggG>ggT	p.G544G	DHX8_ENST00000540306.1_Silent_p.G544G	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	544					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.G544G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		ATGCCTTTGGGGGCAACAAAG	0.498																																					NSCLC(56;1548 1661 49258 49987)												1	Substitution - coding silent(1)	kidney(1)											149.0	150.0	150.0					17																	41582097		2203	4300	6503	SO:0001819	synonymous_variant	1659			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1632G>T	17.37:g.41582097G>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																				0.498	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			
DIO2	1734	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	80669284	80669284	+	Silent	SNP	A	A	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr14:80669284A>G	ENST00000557010.1	-	4	955	c.570T>C	c.(568-570)gaT>gaC	p.D190D	DIO2_ENST00000557125.1_3'UTR|DIO2_ENST00000422005.3_3'UTR|DIO2_ENST00000438257.4_Silent_p.D190D|DIO2_ENST00000555750.1_Silent_p.D226D	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	190					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)	p.D190D(1)|p.D226D(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		CTGCACATCGATCTTCCTGGT	0.552											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					2	Substitution - coding silent(2)	kidney(2)											62.0	66.0	65.0					14																	80669284		2050	4196	6246	SO:0001819	synonymous_variant	1734			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"""thyroxine deiodinase, type II"", ""deiodonase-2"", ""deiodinase-2"""	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.570T>C	14.37:g.80669284A>G		Somatic	1200	WXS	Illumina HiSeq	Phase_I	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Silent	SNP	ENST00000557010.1	37	CCDS45146.1																																																																																				0.552	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			
DIP2A	23181	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	47969770	47969770	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr21:47969770G>A	ENST00000417564.2	+	22	2630	c.2609G>A	c.(2608-2610)aGc>aAc	p.S870N	DIP2A_ENST00000427143.2_Missense_Mutation_p.S806N|DIP2A_ENST00000457905.3_Missense_Mutation_p.S870N|DIP2A_ENST00000400274.1_Missense_Mutation_p.S866N|DIP2A_ENST00000318711.7_Missense_Mutation_p.S871N			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	870					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.S871N(1)|p.S806N(1)|p.S870N(1)		cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAGGAGGACAGCTTCCAGTGG	0.647																																																	3	Substitution - Missense(3)	kidney(3)											69.0	77.0	74.0					21																	47969770		2202	4300	6502	SO:0001583	missense	23181			AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2609G>A	21.37:g.47969770G>A	ENSP00000392066:p.Ser870Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831797	0.91036	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000457905;ENST00000417564	T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84	4.77	4.77	0.60923	.	0.098347	0.64402	D	0.000002	T	0.35595	0.0937	M	0.82056	2.57	0.52501	D	0.999958	D;D;D;D	0.89917	1.0;0.991;0.991;0.999	D;D;D;D	0.87578	0.998;0.917;0.917;0.986	T	0.10245	-1.0638	10	0.37606	T	0.19	-22.0843	17.1613	0.86804	0.0:0.0:1.0:0.0	.	871;806;870;870	E9PER1;E7EMA5;Q14689;Q14689-4	.;.;DIP2A_HUMAN;.	N	866;806;871;870;870	ENSP00000383133:S866N;ENSP00000400528:S806N;ENSP00000323633:S871N;ENSP00000393434:S870N;ENSP00000392066:S870N	ENSP00000323633:S871N	S	+	2	0	DIP2A	46794198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.667000	0.83888	2.355000	0.79922	0.655000	0.94253	AGC		0.647	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1		NM_015151	
DLX2	1746	hgsc.bcm.edu	37	2	172967128	172967129	+	In_Frame_Ins	INS	-	-	GCT	rs201510837|rs376692475	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:172967128_172967129insGCT	ENST00000234198.4	-	1	499_500	c.138_139insAGC	c.(136-141)agcctc>agcAGCctc	p.46_47insS	DLX2_ENST00000466293.2_In_Frame_Ins_p.46_47insS|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	46	Poly-Ser.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GGCTTGTGGAGgctgctgctgc	0.738														113	0.0225639	0.0008	0.0865	5008	,	,		12199	0.0387		0.0109	False		,,,				2504	0.002				GBM(188;775 2993 11256 23072)												0																																										SO:0001652	inframe_insertion	1746			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.136_138dupAGC	2.37:g.172967135_172967137dupGCT	ENSP00000234198:p.Ser46_Ser46dup	Somatic		WXS	Illumina HiSeq	Phase_I	B4DMK4|B7ZA14	In_Frame_Ins	INS	ENST00000234198.4	37	CCDS2248.1																																																																																				0.738	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3			
DNAH14	127602	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	225288466	225288466	+	Intron	SNP	A	A	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:225288466A>G	ENST00000445597.2	+	16	3051				DNAH14_ENST00000430092.1_Silent_p.K1249K|DNAH14_ENST00000439375.2_Silent_p.K1249K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.K1249K(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CCATGTGGAAAAAAATAATGT	0.313																																																	1	Substitution - coding silent(1)	kidney(1)											26.0	25.0	26.0					1																	225288466		692	1585	2277	SO:0001627	intron_variant	127602			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3051+14975A>G	1.37:g.225288466A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	37																																																																																					0.313	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3		XM_059166	
DOCK3	1795	broad.mit.edu;hgsc.bcm.edu	37	3	51246204	51246204	+	Splice_Site	SNP	G	G	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:51246204G>C	ENST00000266037.9	+	13	1060		c.e13-1			NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3						small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.?(2)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TTCTGTTACAGGTGCAACAAC	0.468																																																	2	Unknown(2)	kidney(2)											83.0	87.0	85.0					3																	51246204		2030	4190	6220	SO:0001630	splice_region_variant	1795			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1038-1G>C	3.37:g.51246204G>C		Somatic		WXS	Illumina HiSeq	Phase_I	O15017	Splice_Site	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.627164	0.87560	.	.	ENSG00000088538	ENST00000266037	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0394	0.92992	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DOCK3	51221244	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	9.125000	0.94402	2.878000	0.98634	0.650000	0.86243	.		0.468	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5		NM_004947	Intron
DSPP	1834	broad.mit.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr4:88536919T>C	ENST00000282478.7	+	4	3138	c.3105T>C	c.(3103-3105)gaT>gaC	p.D1035D	DSPP_ENST00000399271.1_Silent_p.D1035D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035D(2)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.517																																																	2	Substitution - coding silent(2)	kidney(2)											63.0	70.0	67.0					4																	88536919		1560	2747	4307	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3105T>C	4.37:g.88536919T>C		Somatic		WXS	Illumina GAIIx	Phase_I	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.517	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3		NM_014208	
DST	667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	56401585	56401585	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:56401585T>C	ENST00000361203.3	-	58	16136	c.16129A>G	c.(16129-16131)Aat>Gat	p.N5377D	DST_ENST00000370769.4_Missense_Mutation_p.N5379D|DST_ENST00000370788.2_Missense_Mutation_p.N3291D|DST_ENST00000370754.5_Missense_Mutation_p.N5557D|DST_ENST00000421834.2_Missense_Mutation_p.N3291D|DST_ENST00000340834.4_5'UTR|DST_ENST00000244364.6_Missense_Mutation_p.N2965D|DST_ENST00000446842.2_Missense_Mutation_p.N5053D|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	5377					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.N5379D(1)|p.N2965D(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACCTTCTTATTGAGAGTCTTC	0.433																																																	2	Substitution - Missense(2)	kidney(2)											136.0	136.0	136.0					6																	56401585		2017	4193	6210	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.16129A>G	6.37:g.56401585T>C	ENSP00000354508:p.Asn5377Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	T	18.73	3.686497	0.68157	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.7	5.7	0.88788	.	0.000000	0.53938	D	0.000045	T	0.58779	0.2146	M	0.80847	2.515	0.25074	N	0.990979	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.997	D;D;D;D;D	0.91635	0.998;0.999;0.998;0.998;0.971	T	0.60637	-0.7224	9	0.12103	T	0.63	.	15.9589	0.79910	0.0:0.0:0.0:1.0	.	3291;5379;5557;5377;2965	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	D	2965;5557;5379;3291;5053;3291;5377	ENSP00000244364:N2965D;ENSP00000359790:N5557D;ENSP00000359805:N5379D;ENSP00000400883:N3291D;ENSP00000393645:N5053D;ENSP00000359824:N3291D;ENSP00000354508:N5377D	ENSP00000244364:N2965D	N	-	1	0	DST	56509544	1.000000	0.71417	0.936000	0.37596	0.703000	0.40648	7.883000	0.87264	2.178000	0.69098	0.477000	0.44152	AAT		0.433	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3		NM_001723	
ECHDC2	55268	broad.mit.edu;hgsc.bcm.edu	37	1	53387308	53387308	+	Missense_Mutation	SNP	G	G	T	rs200668547		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:53387308G>T	ENST00000371522.4	-	1	131	c.38C>A	c.(37-39)cCc>cAc	p.P13H	ECHDC2_ENST00000358358.5_Missense_Mutation_p.P13H|ECHDC2_ENST00000480312.2_5'Flank|ECHDC2_ENST00000541281.1_5'UTR|ECHDC2_ENST00000536120.1_5'UTR	NM_001198961.1	NP_001185890.1	Q86YB7	ECHD2_HUMAN	enoyl CoA hydratase domain containing 2	13					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	lyase activity (GO:0016829)	p.P13H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	12						GGCCCGAAGGGGCCTCCAGGG	0.716																																																	1	Substitution - Missense(1)	kidney(1)											5.0	6.0	5.0					1																	53387308		2029	4146	6175	SO:0001583	missense	55268			AF258590	CCDS571.1, CCDS55600.1, CCDS72794.1	1p32.3	2010-04-30	2010-04-30		ENSG00000121310	ENSG00000121310			23408	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 2"""				Standard	NM_018281		Approved	FLJ10948	uc001cup.4	Q86YB7	OTTHUMG00000008927	ENST00000371522.4:c.38C>A	1.37:g.53387308G>T	ENSP00000360577:p.Pro13His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQ36|Q9NV38	Missense_Mutation	SNP	ENST00000371522.4	37	CCDS55600.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.700677	0.68501	.	.	ENSG00000121310	ENST00000371522;ENST00000358358;ENST00000467988	T;T;T	0.62941	0.18;-0.01;0.0	4.77	2.85	0.33270	.	1.115570	0.06663	N	0.764846	T	0.45736	0.1357	N	0.08118	0	0.22366	N	0.999164	P;P	0.48407	0.855;0.91	B;P	0.47376	0.326;0.545	T	0.30592	-0.9973	10	0.18710	T	0.47	.	6.2081	0.20613	0.0959:0.0:0.7226:0.1815	.	13;13	Q86YB7;Q86YB7-2	ECHD2_HUMAN;.	H	13	ENSP00000360577:P13H;ENSP00000351125:P13H;ENSP00000441962:P13H	ENSP00000351125:P13H	P	-	2	0	ECHDC2	53159896	0.012000	0.17670	0.001000	0.08648	0.334000	0.28698	0.848000	0.27710	0.588000	0.29660	0.555000	0.69702	CCC		0.716	ECHDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024712.3		NM_018281	
EFS	10278	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	23826852	23826852	+	Silent	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr14:23826852C>T	ENST00000216733.3	-	6	1876	c.1269G>A	c.(1267-1269)ggG>ggA	p.G423G	EFS_ENST00000429593.2_Silent_p.G254G|EFS_ENST00000351354.3_Silent_p.G330G|RP11-124D2.3_ENST00000554010.1_RNA	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	423					cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)	p.G423G(1)		endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		CCAGTGGCTCCCCTGGGGACA	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											26.0	31.0	29.0					14																	23826852		2202	4299	6501	SO:0001819	synonymous_variant	10278			AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1269G>A	14.37:g.23826852C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	37	CCDS9595.1																																																																																				0.577	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			
ENAM	10117	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	71495256	71495256	+	Silent	SNP	T	T	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr4:71495256T>G	ENST00000396073.3	+	2	320	c.39T>G	c.(37-39)ccT>ccG	p.P13P		NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	13					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.P13P(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CCTCTTTTCCTAAACTAGATA	0.353																																																	1	Substitution - coding silent(1)	kidney(1)											162.0	175.0	170.0					4																	71495256		2203	4296	6499	SO:0001819	synonymous_variant	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.39T>G	4.37:g.71495256T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																				0.353	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3		NM_031889	
EXOSC9	5393	broad.mit.edu;hgsc.bcm.edu	37	4	122728760	122728760	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr4:122728760T>A	ENST00000243498.5	+	6	696	c.588T>A	c.(586-588)ttT>ttA	p.F196L	EXOSC9_ENST00000512454.1_Missense_Mutation_p.F180L|EXOSC9_ENST00000379663.3_Missense_Mutation_p.F196L|EXOSC9_ENST00000509980.1_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	196	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.F196L(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GTGTCAGTTTTGCCTTTTTCC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											212.0	187.0	196.0					4																	122728760		2203	4300	6503	SO:0001583	missense	5393			M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 1 (75kD)"""	606180	"""polymyositis/scleroderma autoantigen 1, 75kDa"""	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.588T>A	4.37:g.122728760T>A	ENSP00000243498:p.Phe196Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q12883|Q4W5P5|Q86Y41|Q86Y48	Missense_Mutation	SNP	ENST00000243498.5	37	CCDS3722.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.7|27.7	4.854682|4.854682	0.91355|0.91355	.|.	.|.	ENSG00000123737|ENSG00000123737	ENST00000511132|ENST00000243498;ENST00000379663;ENST00000509800;ENST00000512454	.|T;T;T;T	.|0.42513	.|0.97;0.97;0.97;0.97	6.16|6.16	2.48|2.48	0.30137|0.30137	.|Exoribonuclease, phosphorolytic domain 2 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60353|0.60353	0.2262|0.2262	M|M	0.81341|0.81341	2.54|2.54	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D;P	.|0.69078	.|0.997;0.974;0.78	.|D;P;P	.|0.64776	.|0.929;0.688;0.522	T|T	0.60782|0.60782	-0.7195|-0.7195	5|10	.|0.72032	.|D	.|0.01	-17.8904|-17.8904	9.7431|9.7431	0.40431|0.40431	0.0:0.1924:0.0:0.8076|0.0:0.1924:0.0:0.8076	.|.	.|180;196;196	.|D6RIY6;Q06265;Q06265-2	.|.;EXOS9_HUMAN;.	S|L	32|196;196;150;180	.|ENSP00000243498:F196L;ENSP00000368984:F196L;ENSP00000422205:F150L;ENSP00000425782:F180L	.|ENSP00000243498:F196L	C|F	+|+	1|3	0|2	EXOSC9|EXOSC9	122948210|122948210	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.647000|1.647000	0.37260|0.37260	0.214000|0.214000	0.20742|0.20742	0.528000|0.528000	0.53228|0.53228	TGC|TTT		0.363	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2		NM_005033	
FAM174B	400451	broad.mit.edu	37	15	93198679	93198684	+	In_Frame_Del	DEL	TGGAGC	TGGAGC	-	rs66488707|rs111725167|rs68056278	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	TGGAGC	TGGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr15:93198679_93198684delTGGAGC	ENST00000327355.5	-	1	504_509	c.206_211delGCTCCA	c.(205-213)agctccaac>aac	p.SS69del	FAM174B_ENST00000555748.1_5'Flank|FAM174B_ENST00000555696.1_5'Flank	NM_207446.2	NP_997329.2	Q3ZCQ3	F174B_HUMAN	family with sequence similarity 174, member B	69						integral component of membrane (GO:0016021)				endometrium(2)|lung(1)	3						CCACTGCTGTTGGAGCTGGAGCTGCC	0.714														4884	0.97524	0.9092	0.9942	5008	,	,		6551	1.0		1.0	False		,,,				2504	1.0																0										1931,417		927,77,170						2.2	1.0		dbSNP_130	8	5234,70		2614,6,32	no	coding	FAM174B	NM_207446.2		3541,83,202	A1A1,A1R,RR		1.3198,17.7598,6.3643				7165,487				SO:0001651	inframe_deletion	400451				CCDS45355.1	15q26.1	2012-10-03			ENSG00000185442	ENSG00000185442			34339	protein-coding gene	gene with protein product							Standard	NM_207446		Approved	LOC400451, MGC102891	uc010boe.3	Q3ZCQ3	OTTHUMG00000171744	ENST00000327355.5:c.206_211delGCTCCA	15.37:g.93198685_93198690delTGGAGC	ENSP00000329040:p.Ser69_Ser70del	Somatic		WXS	Illumina GAIIx	Phase_I	Q3ZCR9|Q8NBH7	In_Frame_Del	DEL	ENST00000327355.5	37	CCDS45355.1																																																																																				0.714	FAM174B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414931.1		NM_207446	
EVA1A	84141	hgsc.bcm.edu	37	2	75720569	75720577	+	In_Frame_Del	DEL	GCTGTCGCT	GCTGTCGCT	-	rs201833026|rs148155576	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GCTGTCGCT	GCTGTCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:75720569_75720577delGCTGTCGCT	ENST00000233712.1	-	4	681_689	c.244_252delAGCGACAGC	c.(244-252)agcgacagcdel	p.SDS82del	EVA1A_ENST00000410010.1_In_Frame_Del_p.SDS70del|EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000410113.1_In_Frame_Del_p.SDS82del|EVA1A_ENST00000393913.3_In_Frame_Del_p.SDS82del|EVA1A_ENST00000410071.1_In_Frame_Del_p.SDS82del	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	82					apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.D83N(2)									TGCCATCCTCGCTGTCGCTGCTGTCGCTG	0.603														221	0.0441294	0.0772	0.036	5008	,	,		20655	0.001		0.0537	False		,,,				2504	0.0399																2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)							,	303,3963		17,269,1847					,	5.1	1.0		dbSNP_130	60	438,7816		26,386,3715	no	coding,coding	FAM176A	NM_032181.2,NM_001135032.1	,	43,655,5562	A1A1,A1R,RR		5.3065,7.1027,5.9185	,	,		741,11779				SO:0001651	inframe_deletion	0			BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.244_252delAGCGACAGC	2.37:g.75720578_75720586delGCTGTCGCT	ENSP00000233712:p.Ser82_Ser84del	Somatic		WXS	Illumina HiSeq	Phase_I	D6W5J3|Q9HC41	In_Frame_Del	DEL	ENST00000233712.1	37	CCDS1959.1																																																																																				0.603	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1		NM_032181	
FAM182A	284800	broad.mit.edu	37	20	26063625	26063625	+	RNA	SNP	T	T	C	rs77830989		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr20:26063625T>C	ENST00000376398.2	+	0	1142					NR_026713.1		Q5T1J6	F182A_HUMAN	family with sequence similarity 182, member A											breast(1)|endometrium(2)|kidney(1)	4						AGACCTACCATTTCTCGTTAT	0.468																																																	0													54.0	37.0	43.0					20																	26063625		692	1578	2270			284800			AL391119		20p11	2013-03-18	2008-08-05	2008-08-05	ENSG00000125804	ENSG00000125804			16222	other	unknown			"""chromosome 20 open reading frame 91"""	C20orf91			Standard	NR_026713		Approved	bB329D4.1, C20orf91A	uc010gdq.3	Q5T1J6	OTTHUMG00000032144		20.37:g.26063625T>C		Somatic		WXS	Illumina GAIIx	Phase_I	A2RRD0|Q8N947	RNA	SNP	ENST00000376398.2	37																																																																																					0.468	FAM182A-001	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000078473.2			
FAM19A2	338811	broad.mit.edu;ucsc.edu	37	12	62148719	62148719	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr12:62148719C>A	ENST00000416284.3	-	3	1777	c.193G>T	c.(193-195)Gtc>Ttc	p.V65F	FAM19A2_ENST00000550003.1_5'UTR|FAM19A2_ENST00000551449.1_Intron|FAM19A2_ENST00000551619.1_Missense_Mutation_p.V65F	NM_178539.4	NP_848634.1	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A2	65						cytoplasm (GO:0005737)		p.V65F(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	15			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		GAGCACTTGACTGTTTGTGAC	0.493																																																	1	Substitution - Missense(1)	kidney(1)											208.0	141.0	164.0					12																	62148719		2203	4300	6503	SO:0001583	missense	338811			AY325115	CCDS8962.1	12q14.1	2012-10-03			ENSG00000198673	ENSG00000198673			21589	protein-coding gene	gene with protein product						15028294	Standard	NM_178539		Approved	TAFA-2	uc001sqw.3	Q8N3H0	OTTHUMG00000170207	ENST00000416284.3:c.193G>T	12.37:g.62148719C>A	ENSP00000393987:p.Val65Phe	Somatic		WXS	Illumina GAIIx	Phase_I	B3KVV4|Q4G0R9|Q68DK0|Q6GTX6	Missense_Mutation	SNP	ENST00000416284.3	37	CCDS8962.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022680	0.93462	.	.	ENSG00000198673	ENST00000416284;ENST00000551619;ENST00000552075;ENST00000549958;ENST00000548780	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.83385	0.5243	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83650	0.0155	8	.	.	.	.	19.5344	0.95244	0.0:1.0:0.0:0.0	.	65	Q8N3H0	F19A2_HUMAN	F	65;65;66;72;66	.	.	V	-	1	0	FAM19A2	60434986	1.000000	0.71417	0.963000	0.40424	0.971000	0.66376	6.004000	0.70709	2.628000	0.89032	0.558000	0.71614	GTC		0.493	FAM19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407967.2		NM_178539	
FAM47A	158724	broad.mit.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	rs5973088		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:34148877C>G	ENST00000346193.3	-	1	1570	c.1519G>C	c.(1519-1521)Gag>Cag	p.E507Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	507			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.					p.E507Q(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TTGGGAGGCTCCGAGCGGAGA	0.647																																																	1	Substitution - Missense(1)	kidney(1)											29.0	29.0	29.0					X																	34148877		2181	4247	6428	SO:0001583	missense	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1519G>C	X.37:g.34148877C>G	ENSP00000345029:p.Glu507Gln	Somatic		WXS	Illumina GAIIx	Phase_I	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	6	0.003616636528028933	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	9.299	1.052687	0.19907	.	.	ENSG00000185448	ENST00000346193	T	0.14391	2.51	0.226	0.226	0.15353	.	.	.	.	.	T	0.05227	0.0139	L	0.27053	0.805	0.09310	N	1	B	0.24483	0.104	B	0.16722	0.016	T	0.41466	-0.9507	8	0.17832	T	0.49	.	.	.	.	rs5973088	507	Q5JRC9	FA47A_HUMAN	Q	507	ENSP00000345029:E507Q	ENSP00000345029:E507Q	E	-	1	0	FAM47A	34058798	0.053000	0.20554	0.000000	0.03702	0.001000	0.01503	1.713000	0.37951	0.283000	0.22279	0.287000	0.19450	GAG		0.647	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1		NM_203408	
GALNT13	114805	broad.mit.edu;ucsc.edu	37	2	155115568	155115568	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:155115568G>T	ENST00000392825.3	+	8	1459	c.892G>T	c.(892-894)Gac>Tac	p.D298Y	GALNT13_ENST00000487047.1_3'UTR|GALNT13_ENST00000409237.1_Missense_Mutation_p.D298Y	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	298	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.D298Y(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						ATTTTCTATTGACAGAAACTA	0.343																																																	1	Substitution - Missense(1)	kidney(1)											88.0	94.0	92.0					2																	155115568		2203	4300	6503	SO:0001583	missense	114805			AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.892G>T	2.37:g.155115568G>T	ENSP00000376570:p.Asp298Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	37	CCDS2199.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.921990	0.92319	.	.	ENSG00000144278	ENST00000392825;ENST00000409237	T;T	0.59906	0.23;0.23	5.85	5.85	0.93711	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.82254	0.4997	M	0.92219	3.285	0.80722	D	1	D;D;D;D	0.76494	0.973;0.998;0.99;0.999	P;D;D;D	0.71870	0.818;0.96;0.917;0.975	D	0.85845	0.1400	10	0.87932	D	0	.	19.1513	0.93491	0.0:0.0:1.0:0.0	.	298;298;298;298	Q8IUC8-2;B3KY85;Q08ER7;Q8IUC8	.;.;.;GLT13_HUMAN	Y	298	ENSP00000376570:D298Y;ENSP00000387239:D298Y	ENSP00000376570:D298Y	D	+	1	0	GALNT13	154823814	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.863000	0.87023	2.772000	0.95346	0.650000	0.86243	GAC		0.343	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2		NM_052917	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739938	20739943	+	In_Frame_Del	DEL	CTCCTG	CTCCTG	-	rs201222558		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	CTCCTG	CTCCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr15:20739938_20739943delCTCCTG	ENST00000427390.2	-	8	1897_1902	c.1807_1812delCAGGAG	c.(1807-1812)caggagdel	p.QE603del		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	603	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						acatcttctcctcctgctcctgcctc	0.553																																																	0										8,1308		2,4,652							0.0			5	46,2864		5,36,1414	no	coding	GOLGA6L6	NM_001145004.1		7,40,2066	A1A1,A1R,RR		1.5808,0.6079,1.2778				54,4172				SO:0001651	inframe_deletion	727832			AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1807_1812delCAGGAG	15.37:g.20739944_20739949delCTCCTG	ENSP00000398615:p.Gln603_Glu604del	Somatic		WXS	Illumina HiSeq	Phase_I	D3YTC0	In_Frame_Del	DEL	ENST00000427390.2	37	CCDS45184.1																																																																																				0.553	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3		NM_001145004	
GOLGA6L17P	642402	broad.mit.edu	37	15	85053208	85053208	+	RNA	SNP	A	A	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr15:85053208A>C	ENST00000414190.2	-	0	244					NR_003246.2																						AAAGAATGGCATGCAGCCTCT	0.512																																																	0																																												374650																															15.37:g.85053208A>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000414190.2	37																																																																																					0.512	GOLGA6L5-003	KNOWN	mRNA_end_NF|basic	processed_transcript	pseudogene	OTTHUMT00000418579.1			
HLA-C	3107	hgsc.bcm.edu	37	6	31238179	31238179	+	Missense_Mutation	SNP	C	C	T	rs41562012	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:31238179C>T	ENST00000376228.5	-	4	717	c.703G>A	c.(703-705)Gcg>Acg	p.A235T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A235T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	235	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTGATCTCCGCAGGGTAGAAG	0.627													c|||	83	0.0165735	0.0136	0.0202	5008	,	,		16224	0.001		0.0437	False		,,,				2504	0.0061																0								C	THR/ALA	53,4353		0,53,2150	41.0	42.0	42.0		703	1.8	0.3	6	dbSNP_127	42	340,8250		5,330,3960	no	missense	HLA-C	NM_002117.5	58	5,383,6110	TT,TC,CC		3.9581,1.2029,3.024	possibly-damaging	235/367	31238179	393,12603	2203	4295	6498	SO:0001583	missense	3107			M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.703G>A	6.37:g.31238179C>T	ENSP00000365402:p.Ala235Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	41	0.018772893772893772	7	0.014227642276422764	5	0.013812154696132596	1	0.0017482517482517483	28	0.036939313984168866	.	4.284	0.051806	0.08291	0.012029	0.039581	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.14766	2.48;2.48	2.67	1.79	0.24919	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.402896	0.17690	U	0.165292	T	0.14830	0.0358	H	0.97758	4.07	0.09310	N	1	B;B;B;B	0.19200	0.034;0.001;0.004;0.009	B;B;B;B	0.28232	0.087;0.013;0.022;0.017	T	0.23726	-1.0180	10	0.87932	D	0	.	5.5522	0.17097	0.0:0.84:0.0:0.16	rs41562012	235;235;235;235	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	T	235;235;235;272	ENSP00000365402:A235T;ENSP00000372819:A235T	ENSP00000365402:A235T	A	-	1	0	HLA-C	31346158	0.000000	0.05858	0.342000	0.25602	0.447000	0.32167	-1.515000	0.02252	0.702000	0.31825	0.298000	0.19748	GCG		0.627	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3		NM_002117	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	rs371382486|rs55976345|rs541496808|rs199726261|rs548996855|rs112569629|rs201613510	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENST00000530275.1	+	1	3247_3285	c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	c.(3052-3090)gaggaatccgcctccgcagctgttgcagtgcccacccccdel	p.EESASAAVAVPTP1018del	MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1018	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GCCCACCCCAGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCCGAGGAATCTG	0.682																																																	0									,,	832,2850		248,336,1257					,,	0.0	0.0			18	1888,6000		448,992,2504	no	intron,coding,intron	MACF1,KIAA0754	NM_033044.3,NM_015038.1,NM_012090.4	,,	696,1328,3761	A1A1,A1R,RR		23.9351,22.5964,23.5091	,,	,,		2720,8850				SO:0001651	inframe_deletion	643314					1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	1.37:g.39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENSP00000431179:p.Glu1018_Pro1030del	Somatic		WXS	Illumina HiSeq	Phase_I	E9PMC2|Q6ZSB2	In_Frame_Del	DEL	ENST00000530275.1	37																																																																																					0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1		NM_015038	
KCND3	3752	broad.mit.edu	37	1	112524688	112524688	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:112524688G>A	ENST00000315987.2	-	2	1140	c.661C>T	c.(661-663)Cgc>Tgc	p.R221C	KCND3_ENST00000302127.4_Missense_Mutation_p.R221C|KCND3_ENST00000369697.1_Missense_Mutation_p.R221C	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	221					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.R221C(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	ACCGAGTAGCGCTCCCCGCAC	0.657																																																	1	Substitution - Missense(1)	kidney(1)											29.0	30.0	30.0					1																	112524688		2203	4300	6503	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6239	protein-coding gene	gene with protein product		605411	"""spinocerebellar ataxia 22"", ""spinocerebellar ataxia 19"""	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.661C>T	1.37:g.112524688G>A	ENSP00000319591:p.Arg221Cys	Somatic		WXS	Illumina GAIIx	Phase_I	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361302	0.61403	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.97553	-4.43;-4.43;-4.43	5.51	4.6	0.57074	.	0.047080	0.85682	N	0.000000	D	0.97133	0.9063	M	0.84326	2.69	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.59357	0.772;0.856	D	0.97265	0.9907	10	0.87932	D	0	.	7.5446	0.27759	0.0817:0.0:0.6508:0.2675	.	221;221	Q14D71;Q9UK17	.;KCND3_HUMAN	C	221	ENSP00000358711:R221C;ENSP00000319591:R221C;ENSP00000306923:R221C	ENSP00000306923:R221C	R	-	1	0	KCND3	112326211	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.285000	0.58989	1.335000	0.45486	0.563000	0.77884	CGC		0.657	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1		NM_172198	
NYAP2	57624	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	226378271	226378271	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:226378271C>T	ENST00000272907.6	+	3	819	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	136					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.R136W(1)									CTGTGGCTCACGGAGACAACC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											60.0	74.0	69.0					2																	226378271		2100	4235	6335	SO:0001583	missense	0			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.406C>T	2.37:g.226378271C>T	ENSP00000272907:p.Arg136Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184690	0.57909	.	.	ENSG00000144460	ENST00000272907	T	0.52057	0.68	5.42	2.49	0.30216	.	0.000000	0.64402	D	0.000003	T	0.68210	0.2976	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.71481	-0.4580	10	0.72032	D	0.01	-15.3207	14.8854	0.70564	0.4886:0.5114:0.0:0.0	.	136	Q9P242	K1486_HUMAN	W	136	ENSP00000272907:R136W	ENSP00000272907:R136W	R	+	1	2	KIAA1486	226086515	1.000000	0.71417	0.831000	0.32960	0.751000	0.42716	2.299000	0.43611	0.201000	0.20466	-0.309000	0.09137	CGG		0.577	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1		NM_020864	
KRT2	3849	hgsc.bcm.edu	37	12	53045597	53045597	+	Silent	SNP	A	A	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr12:53045597A>T	ENST00000309680.3	-	1	351	c.330T>A	c.(328-330)ggT>ggA	p.G110G		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	110	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		cgaaaccaccaccactgaagc	0.637																																																	0													43.0	28.0	33.0					12																	53045597		2195	4287	6482	SO:0001819	synonymous_variant	3849				CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.330T>A	12.37:g.53045597A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q4VAQ2	Silent	SNP	ENST00000309680.3	37	CCDS8835.1																																																																																				0.637	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1		NM_000423	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012219	46012220	+	In_Frame_Ins	INS	-	-	GGGGCGCAGCAGCTG	rs374776064|rs587611810|rs71199613	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr21:46012219_46012220insGGGGCGCAGCAGCTG	ENST00000400368.1	-	1	166_167	c.146_147insCAGCTGCTGCGCCCC	c.(145-147)ccg>ccCAGCTGCTGCGCCCCg	p.49_49P>PSCCAP	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	49	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGCAGGGGGCCGGGGCGCAGCA	0.688														1042	0.208067	0.1188	0.2522	5008	,	,		15055	0.1379		0.3231	False		,,,				2504	0.2515																0																																										SO:0001652	inframe_insertion	386674			AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.146_147insCAGCTGCTGCGCCCC	21.37:g.46012219_46012220insGGGGCGCAGCAGCTG	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Ins	INS	ENST00000400368.1	37	CCDS42959.1																																																																																				0.688	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1		NM_198688	
KRTAP1-1	81851	broad.mit.edu;ucsc.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr17:39197549G>C	ENST00000306271.4	-	1	164	c.101C>G	c.(100-102)tCc>tGc	p.S34C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612																																																	6	Substitution - Missense(6)	kidney(4)|lung(1)|prostate(1)											49.0	62.0	58.0					17																	39197549		2018	4199	6217	SO:0001583	missense	81851			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.101C>G	17.37:g.39197549G>C	ENSP00000305975:p.Ser34Cys	Somatic		WXS	Illumina GAIIx	Phase_I	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	G	0.085	-1.176298	0.01646	.	.	ENSG00000188581	ENST00000306271	T	0.16196	2.36	3.91	1.65	0.23941	.	.	.	.	.	T	0.01835	0.0058	N	0.00010	-3.04	0.22552	N	0.998996	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.02654	T	1	.	7.8006	0.29172	0.1777:0.6415:0.1808:0.0	.	34	Q07627	KRA11_HUMAN	C	34	ENSP00000305975:S34C	ENSP00000305975:S34C	S	-	2	0	KRTAP1-1	36451075	1.000000	0.71417	0.987000	0.45799	0.816000	0.46133	1.227000	0.32576	0.919000	0.36945	-0.233000	0.12211	TCC		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1		NM_030967	
KRTAP5-2	440021	hgsc.bcm.edu	37	11	1619173	1619202	+	In_Frame_Del	DEL	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	-	rs61869706|rs199811378|rs36134435|rs61869704|rs59506446	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	CCCCCACAGGAGCCACAGCCCCCCTTGGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:1619173_1619202delCCCCCACAGGAGCCACAGCCCCCCTTGGAG	ENST00000412090.1	-	1	322_351	c.279_308delCTCCAAGGGGGGCTGTGGCTCCTGTGGGGG	c.(277-309)ggctccaaggggggctgtggctcctgtgggggt>ggt	p.93_103GSKGGCGSCGG>G	KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	93	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCTTGGAACCCCCACAGGAGCCACAGCCCCCCTTGGAGCCCCCACAGG	0.657																																																	0																																										SO:0001651	inframe_deletion	440021			AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"""Keratin associated proteins"""	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.279_308delCTCCAAGGGGGGCTGTGGCTCCTGTGGGGG	11.37:g.1619173_1619202delCCCCCACAGGAGCCACAGCCCCCCTTGGAG	ENSP00000400041:p.Gly103_Gly112del	Somatic		WXS	Illumina HiSeq	Phase_I	A9JTZ1	In_Frame_Del	DEL	ENST00000412090.1	37	CCDS31331.1																																																																																				0.657	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1		NM_001004325	
LRRC8B	23507	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	90049487	90049487	+	Silent	SNP	T	T	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:90049487T>C	ENST00000330947.2	+	5	1638	c.1278T>C	c.(1276-1278)ctT>ctC	p.L426L	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.L426L|LRRC8B_ENST00000439853.1_Silent_p.L426L	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	426					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L426L(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		AACTGCATCTTTTTATGCTCA	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											73.0	76.0	75.0					1																	90049487		2203	4300	6503	SO:0001819	synonymous_variant	23507			AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.1278T>C	1.37:g.90049487T>C		Somatic		WXS	Illumina HiSeq	Phase_I	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																				0.418	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1		NM_015350	
LTF	4057	broad.mit.edu	37	3	46477692	46477692	+	Silent	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:46477692C>T	ENST00000231751.4	-	17	2422	c.2127G>A	c.(2125-2127)agG>agA	p.R709R	LTF_ENST00000417439.1_Silent_p.R707R|LTF_ENST00000493056.1_5'Flank|LTF_ENST00000426532.2_Silent_p.R665R	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	709					antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)	p.R709R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GGTTTTACTTCCTGAGGAATT	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											114.0	113.0	113.0					3																	46477692		2203	4296	6499	SO:0001819	synonymous_variant	4057				CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.2127G>A	3.37:g.46477692C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																				0.502	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2		NM_002343	
KMT2C	58508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	151860719	151860719	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr7:151860719G>A	ENST00000262189.6	-	43	10161	c.9943C>T	c.(9943-9945)Cag>Tag	p.Q3315*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.Q3315*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3315	Gln-rich.|Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Q3315*(2)									GTTGTGTGCTGCTGGTGCTGA	0.582																																																	2	Substitution - Nonsense(2)	kidney(2)											142.0	120.0	128.0					7																	151860719		2203	4300	6503	SO:0001587	stop_gained	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.9943C>T	7.37:g.151860719G>A	ENSP00000262189:p.Gln3315*	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	53|53	20.299640|20.299640	0.99929|0.99929	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193	.|.	.|.	.|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	.|0.000000	.|0.42548	.|D	.|0.000693	T|.	0.65026|.	0.2652|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.59402|.	-0.7461|.	4|.	.|0.19147	.|T	.|0.46	.|.	16.5202|16.5202	0.84312|0.84312	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	820|3315	.|.	.|ENSP00000262189:Q3315X	A|Q	-|-	2|1	0|0	MLL3|MLL3	151491652|151491652	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	6.709000|6.709000	0.74665|0.74665	2.322000|2.322000	0.78497|0.78497	0.655000|0.655000	0.94253|0.94253	GCA|CAG		0.582	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			
MMP21	118856	broad.mit.edu;hgsc.bcm.edu	37	10	127461203	127461203	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr10:127461203C>T	ENST00000368808.3	-	3	813	c.814G>A	c.(814-816)Gac>Aac	p.D272N		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	272					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D272N(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	ATGCCCGTGTCACTGGTGGGA	0.572																																																	1	Substitution - Missense(1)	kidney(1)											164.0	141.0	149.0					10																	127461203		2203	4300	6503	SO:0001583	missense	118856			AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"""matrix metalloproteinase 21"""			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.814G>A	10.37:g.127461203C>T	ENSP00000357798:p.Asp272Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.332655	0.60853	.	.	ENSG00000154485	ENST00000368808	T	0.21543	2.0	4.51	3.6	0.41247	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.378221	0.28583	N	0.014826	T	0.15998	0.0385	L	0.31926	0.97	0.36382	D	0.861964	B	0.30068	0.267	B	0.31495	0.131	T	0.15407	-1.0438	10	0.20046	T	0.44	-22.293	12.2147	0.54400	0.0:0.8268:0.1732:0.0	.	272	Q8N119	MMP21_HUMAN	N	272	ENSP00000357798:D272N	ENSP00000357798:D272N	D	-	1	0	MMP21	127451193	0.990000	0.36364	0.392000	0.26245	0.969000	0.65631	4.493000	0.60341	1.105000	0.41606	0.561000	0.74099	GAC		0.572	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			
MUC21	394263	hgsc.bcm.edu	37	6	30954485	30954485	+	Missense_Mutation	SNP	G	G	A	rs140951082	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:30954485G>A	ENST00000376296.3	+	2	774	c.533G>A	c.(532-534)aGc>aAc	p.S178N	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	178	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S178N(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTGGGGCCAGCACAGCCACC	0.617													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		28215	0.0		0.005	False		,,,				2504	0.001																1	Substitution - Missense(1)	NS(1)											150.0	143.0	145.0					6																	30954485		2202	4299	6501	SO:0001583	missense	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.533G>A	6.37:g.30954485G>A	ENSP00000365473:p.Ser178Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.277242	0.23307	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02863	4.13	3.72	-3.6	0.04570	.	.	.	.	.	T	0.00608	0.0020	L	0.34521	1.04	0.09310	N	1	B	0.16802	0.019	B	0.19946	0.027	T	0.48198	-0.9056	8	.	.	.	-1.0525	1.0899	0.01661	0.3623:0.2667:0.2352:0.1358	.	178	Q5SSG8	MUC21_HUMAN	N	178	ENSP00000365473:S178N	.	S	+	2	0	MUC21	31062464	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-2.096000	0.01349	-0.539000	0.06273	-0.330000	0.08379	AGC		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3		NM_001010909	
MUC21	394263	hgsc.bcm.edu	37	6	30955115	30955115	+	Missense_Mutation	SNP	G	G	A	rs52826894		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:30955115G>A	ENST00000376296.3	+	2	1404	c.1163G>A	c.(1162-1164)aGc>aAc	p.S388N	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	388	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTGGGGCCAGCACAGCCACC	0.647																																																	0													141.0	138.0	139.0					6																	30955115		2203	4295	6498	SO:0001583	missense	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1163G>A	6.37:g.30955115G>A	ENSP00000365473:p.Ser388Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	g	12.57	1.977763	0.34848	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03441	3.93	4.44	2.59	0.31030	.	.	.	.	.	T	0.01156	0.0038	L	0.29908	0.895	0.09310	N	1	P	0.41784	0.762	B	0.41571	0.36	T	0.48990	-0.8985	9	0.41790	T	0.15	-1.1429	4.453	0.11630	0.2014:0.1881:0.6105:0.0	rs9262396;rs9262396	388	Q5SSG8	MUC21_HUMAN	N	238;388	ENSP00000365473:S388N	ENSP00000365473:S388N	S	+	2	0	MUC21	31063094	0.000000	0.05858	0.016000	0.15963	0.116000	0.19942	-0.228000	0.09114	0.578000	0.29487	0.586000	0.80456	AGC		0.647	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3		NM_001010909	
MUC21	394263	hgsc.bcm.edu	37	6	30955140	30955140	+	Silent	SNP	C	C	T	rs143388506	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr6:30955140C>T	ENST00000376296.3	+	2	1429	c.1188C>T	c.(1186-1188)agC>agT	p.S396S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	396	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTGAGTCCAGCACGACCTCCA	0.627																																																	0													141.0	138.0	139.0					6																	30955140		2201	4298	6499	SO:0001819	synonymous_variant	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1188C>T	6.37:g.30955140C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																				0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3		NM_001010909	
MUC4	4585	broad.mit.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	rs541438739	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195506983G>A	ENST00000463781.3	-	2	11927	c.11468C>T	c.(11467-11469)aCc>aTc	p.T3823I	MUC4_ENST00000475231.1_Missense_Mutation_p.T3823I|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3823I(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGGGTGGTGTCACC	0.587													.|||	248	0.0495208	0.1399	0.0317	5008	,	,		9423	0.002		0.0358	False		,,,				2504	0.0031																1	Substitution - Missense(1)	kidney(1)											5.0	5.0	5.0					3																	195506983		440	1246	1686	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11468C>T	3.37:g.195506983G>A	ENSP00000417498:p.Thr3823Ile	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.889	0.533565	0.13188	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.55	.	.	.	.	.	.	.	.	T	0.13200	0.0320	N	0.14661	0.345	0.09310	N	1	P	0.47604	0.898	B	0.36885	0.235	T	0.15838	-1.0423	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3695	E7ESK3	.	I	3823	ENSP00000417498:T3823I;ENSP00000420243:T3823I	.	T	-	2	0	MUC4	196991762	0.000000	0.05858	0.110000	0.21437	0.111000	0.19643	-0.374000	0.07484	0.064000	0.16427	0.064000	0.15345	ACC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195507717	195507717	+	Silent	SNP	G	G	T	rs376353447		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195507717G>T	ENST00000463781.3	-	2	11193	c.10734C>A	c.(10732-10734)tcC>tcA	p.S3578S	MUC4_ENST00000475231.1_Silent_p.S3578S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S3578S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTCACCTGTGGATACTGAGG	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											8.0	8.0	8.0					3																	195507717		621	1507	2128	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10734C>A	3.37:g.195507717G>T		Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195508500	195508500	+	Missense_Mutation	SNP	G	G	C	rs374619108		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195508500G>C	ENST00000463781.3	-	2	10410	c.9951C>G	c.(9949-9951)gaC>gaG	p.D3317E	MUC4_ENST00000475231.1_Missense_Mutation_p.D3317E|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.D3317E(2)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)|p.S3317R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAA	0.577																																																	5	Substitution - Missense(3)|Deletion - In frame(2)	stomach(4)|kidney(1)											9.0	12.0	11.0					3																	195508500		600	1514	2114	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9951C>G	3.37:g.195508500G>C	ENSP00000417498:p.Asp3317Glu	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.278	0.419423	0.11928	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30981	1.61;1.51	0.423	0.423	0.16463	.	.	.	.	.	T	0.14141	0.0342	N	0.19112	0.55	0.09310	N	1	P	0.43352	0.804	B	0.33196	0.159	T	0.14144	-1.0483	7	.	.	.	.	.	.	.	.	3189	E7ESK3	.	E	3317	ENSP00000417498:D3317E;ENSP00000420243:D3317E	.	D	-	3	2	MUC4	196993279	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.672000	0.25187	0.494000	0.27859	0.089000	0.15464	GAC		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195511525	195511526	+	Missense_Mutation	DNP	TC	TC	CT	rs200787582|rs199709753	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195511525_195511526TC>CT	ENST00000463781.3	-	2	7384_7385	c.6925_6926GA>AG	c.(6925-6927)GAc>AGc	p.D2309S	MUC4_ENST00000475231.1_Missense_Mutation_p.D2309S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.D2309N(3)|p.D2309G(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGCGTCGGTGACATGA	0.584																																																	5	Substitution - Missense(5)	kidney(3)|stomach(2)																																								SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6925_6926delinsCT	3.37:g.195511525_195511526delinsCT	ENSP00000417498:p.Asp2309Ser	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.584	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195506487	195506534	+	In_Frame_Del	DEL	GGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	GGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	-	rs560897359|rs542643120|rs72499648|rs201186756|rs546685353|rs566561255|rs187734372|rs202207620|rs202026273|rs199874579|rs530867213|rs200996132|rs545209449|rs563397158|rs199960521|rs536593912|rs532552592|rs374482509	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	GGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195506487_195506534delGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	ENST00000463781.3	-	2	12376_12423	c.11917_11964delAGCCGTTCCTCAGCATCCACAGGTCACGCCACCCCCCTTCCTGTCACC	c.(11917-11964)agccgttcctcagcatccacaggtcacgccaccccccttcctgtcaccdel	p.SRSSASTGHATPLPVT3973del	MUC4_ENST00000475231.1_In_Frame_Del_p.SRSSASTGHATPLPVT3973del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P3984P(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCTGGTGACAGGA	0.593																																																	1	Substitution - coding silent(1)	stomach(1)																																								SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11917_11964delAGCCGTTCCTCAGCATCCACAGGTCACGCCACCCCCCTTCCTGTCACC	3.37:g.195506487_195506534delGGTGACAGGAAGGGGGGTGGCGTGACCTGTGGATGCTGAGGAACGGCT	ENSP00000417498:p.Ser3973_Thr3988del	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.593	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu;hgsc.bcm.edu	37	3	195507915	195507915	+	Silent	SNP	T	T	C	rs71635073		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195507915T>C	ENST00000463781.3	-	2	10995	c.10536A>G	c.(10534-10536)tcA>tcG	p.S3512S	MUC4_ENST00000475231.1_Silent_p.S3512S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S3512S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGGTGGATGCTGAGGAAGCGC	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											45.0	38.0	40.0					3																	195507915		649	1586	2235	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10536A>G	3.37:g.195507915T>C		Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu;hgsc.bcm.edu	37	3	195509563	195509563	+	Missense_Mutation	SNP	A	A	T	rs28605870		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195509563A>T	ENST00000463781.3	-	2	9347	c.8888T>A	c.(8887-8889)gTc>gAc	p.V2963D	MUC4_ENST00000475231.1_Missense_Mutation_p.V2963D|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V2963D(5)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGACAGGAAGAGA	0.587																																																	5	Substitution - Missense(5)	kidney(2)|skin(2)|endometrium(1)											8.0	7.0	7.0					3																	195509563		603	1454	2057	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8888T>A	3.37:g.195509563A>T	ENSP00000417498:p.Val2963Asp	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	5.292	0.239303	0.10023	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	.	.	.	.	.	.	.	.	T	0.28366	0.0701	N	0.19112	0.55	0.09310	N	1	D	0.65815	0.995	D	0.68483	0.958	T	0.11372	-1.0590	7	.	.	.	.	1.4974	0.02469	0.4322:0.0:0.2571:0.3107	rs60024035	2835	E7ESK3	.	D	2963	ENSP00000417498:V2963D;ENSP00000420243:V2963D	.	V	-	2	0	MUC4	196994342	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.570000	0.02140	-0.942000	0.03695	0.000000	0.15137	GTC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195511993	195511993	+	Missense_Mutation	SNP	A	A	G	rs3107749	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195511993A>G	ENST00000463781.3	-	2	6917	c.6458T>C	c.(6457-6459)gTa>gCa	p.V2153A	MUC4_ENST00000475231.1_Missense_Mutation_p.V2153A|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGT	0.567													.|||	2081	0.415535	0.1868	0.4092	5008	,	,		7614	0.6865		0.4801	False		,,,				2504	0.3834																0													16.0	11.0	12.0					3																	195511993		674	1534	2208	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6458T>C	3.37:g.195511993A>G	ENSP00000417498:p.Val2153Ala	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	2.897	-0.228402	0.06022	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.36;1.39	.	.	.	.	.	.	.	.	T	0.10165	0.0249	N	0.02539	-0.55	0.18873	N	0.999984	P	0.37985	0.613	B	0.25140	0.058	T	0.14839	-1.0458	7	.	.	.	.	5.1997	0.15256	0.9998:0.0:2.0E-4:0.0	.	2153	E7ESK3	.	A	2153	ENSP00000417498:V2153A;ENSP00000420243:V2153A	.	V	-	2	0	MUC4	196996388	0.000000	0.05858	0.028000	0.17463	0.096000	0.18686	-0.307000	0.08167	0.408000	0.25621	0.055000	0.15244	GTA		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195513826	195513826	+	Missense_Mutation	SNP	G	G	A	rs202029925		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:195513826G>A	ENST00000463781.3	-	2	5084	c.4625C>T	c.(4624-4626)cCt>cTt	p.P1542L	MUC4_ENST00000475231.1_Missense_Mutation_p.P1542L|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.P1542L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGGGCTAGTGAC	0.592																																																	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)																																								SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4625C>T	3.37:g.195513826G>A	ENSP00000417498:p.Pro1542Leu	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	9.599	1.128178	0.20959	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26067	1.77;1.76	0.844	0.844	0.18943	.	.	.	.	.	T	0.21307	0.0513	N	0.19112	0.55	0.31987	N	0.6051	P	0.48350	0.909	P	0.52909	0.713	T	0.25779	-1.0122	8	.	.	.	.	5.3481	0.16020	1.0E-4:0.0:0.9999:0.0	.	1542	E7ESK3	.	L	1542	ENSP00000417498:P1542L;ENSP00000420243:P1542L	.	P	-	2	0	MUC4	196998221	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-0.058000	0.11750	0.088000	0.17205	0.089000	0.15464	CCT		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYH1	4619	broad.mit.edu;hgsc.bcm.edu	37	17	10419922	10419922	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr17:10419922G>A	ENST00000226207.5	-	3	132	c.38C>T	c.(37-39)gCt>gTt	p.A13V	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	13					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A13V(1)|p.A13D(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						GAAAGGAGCAGCCTCCCCAAA	0.502																																																	2	Substitution - Missense(2)	lung(1)|kidney(1)											79.0	74.0	76.0					17																	10419922		2203	4300	6503	SO:0001583	missense	4619				CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.38C>T	17.37:g.10419922G>A	ENSP00000226207:p.Ala13Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	G	34	5.377028	0.95945	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	D	0.87966	-2.32	5.36	5.36	0.76844	.	0.000000	0.42964	U	0.000640	D	0.92990	0.7769	M	0.86502	2.82	0.80722	D	1	D	0.59767	0.986	P	0.54889	0.763	D	0.93901	0.7188	10	0.87932	D	0	.	19.2789	0.94044	0.0:0.0:1.0:0.0	.	13	P12882	MYH1_HUMAN	V	13	ENSP00000226207:A13V	ENSP00000226207:A13V	A	-	2	0	MYH1	10360647	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.636000	0.98440	2.774000	0.95407	0.655000	0.94253	GCT		0.502	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1		NM_005963	
NBPF10	100132406	broad.mit.edu	37	1	145296448	145296448	+	Missense_Mutation	SNP	T	T	A	rs4996268		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:145296448T>A	ENST00000342960.5	+	3	405	c.370T>A	c.(370-372)Tat>Aat	p.Y124N	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	124						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.Y124N(2)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CCGCTCATTGTATGAGCATCT	0.562																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.370T>A	1.37:g.145296448T>A	ENSP00000345684:p.Tyr124Asn	Somatic		WXS	Illumina GAIIx	Phase_I	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.880827	0.00061	.	.	ENSG00000163386	ENST00000369339;ENST00000448873;ENST00000342960	T	0.02552	4.25	1.04	-2.09	0.07232	.	.	.	.	.	T	0.00109	0.0003	N	0.00075	-2.25	0.09310	N	1	.	.	.	.	.	.	T	0.35351	-0.9792	7	0.02654	T	1	.	3.206	0.06666	0.3078:0.4616:0.0:0.2307	rs4996268	.	.	.	N	124;49;124	ENSP00000345684:Y124N	ENSP00000345684:Y124N	Y	+	1	0	NBPF10	144007805	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.048000	0.14078	-3.520000	0.00148	-3.904000	0.00016	TAT		0.562	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001039703	
NBPF10	100132406	broad.mit.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	A	T	rs75252120	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:145323656A>T	ENST00000342960.5	+	27	3528	c.3493A>T	c.(3493-3495)Att>Ttt	p.I1165F	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	752						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I1165F(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473																																																	3	Substitution - Missense(3)	endometrium(2)|kidney(1)																																								SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.3493A>T	1.37:g.145323656A>T	ENSP00000345684:p.Ile1165Phe	Somatic		WXS	Illumina GAIIx	Phase_I	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	7.524	0.657305	0.14580	.	.	ENSG00000163386	ENST00000342960	T	0.03441	3.93	.	.	.	.	.	.	.	.	T	0.02342	0.0072	M	0.67953	2.075	0.09310	N	1	.	.	.	.	.	.	T	0.44065	-0.9352	5	0.28530	T	0.3	.	.	.	.	.	.	.	.	F	1165	ENSP00000345684:I1165F	ENSP00000345684:I1165F	I	+	1	0	NBPF10	144035013	0.353000	0.24904	0.005000	0.12908	0.123000	0.20343	1.122000	0.31295	0.386000	0.24997	0.128000	0.15822	ATT		0.473	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001039703	
NCOR2	9612	hgsc.bcm.edu	37	12	124887096	124887096	+	Silent	SNP	T	T	C	rs3040832		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr12:124887096T>C	ENST00000405201.1	-	14	1494	c.1494A>G	c.(1492-1494)caA>caG	p.Q498Q	NCOR2_ENST00000404621.1_Silent_p.Q497Q|NCOR2_ENST00000397355.1_Silent_p.Q498Q|NCOR2_ENST00000429285.2_Silent_p.Q497Q|NCOR2_ENST00000356219.3_Silent_p.Q498Q|NCOR2_ENST00000404121.2_Silent_p.Q68Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	498	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gctgctgctgttgttgctgct	0.617																																																	0													9.0	10.0	10.0					12																	124887096		2047	4186	6233	SO:0001819	synonymous_variant	9612			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1494A>G	12.37:g.124887096T>C		Somatic		WXS	Illumina HiSeq	Phase_I	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																				0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2		NM_006312	
NEFH	4744	hgsc.bcm.edu	37	22	29885589	29885590	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT	rs200984527|rs267607533		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr22:29885589_29885590insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1993_1994	c.1960_1961insCCCCTGAGAAGGCCAAGT	c.(1960-1962)tcc>tCCCCTGAGAAGGCCAAGTcc	p.654_654S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	660	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGGCCAAGTCCCCAGAGAAG	0.559																																																	0																																										SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	22.37:g.29885589_29885590insCCCCTGAGAAGGCCAAGT	ENSP00000311997:p.ProGluLysAlaLysSer654dup	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				0.559	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2		NM_021076	
NYNRIN	57523	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	24884470	24884470	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr14:24884470C>T	ENST00000382554.3	+	9	3833	c.3515C>T	c.(3514-3516)aCg>aTg	p.T1172M		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1172					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.T1172M(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GTGGCCCTGACGGCCATCCTC	0.657																																																	1	Substitution - Missense(1)	kidney(1)											58.0	66.0	64.0					14																	24884470		2084	4197	6281	SO:0001583	missense	57523			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.3515C>T	14.37:g.24884470C>T	ENSP00000371994:p.Thr1172Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.890363	0.52014	.	.	ENSG00000205978	ENST00000382554	T	0.45276	0.9	4.61	4.61	0.57282	.	.	.	.	.	T	0.47544	0.1451	N	0.19112	0.55	0.29198	N	0.875415	D	0.89917	1.0	D	0.66497	0.944	T	0.43605	-0.9381	9	0.72032	D	0.01	.	12.8162	0.57667	0.0:1.0:0.0:0.0	.	1172	Q9P2P1	NYNRI_HUMAN	M	1172	ENSP00000371994:T1172M	ENSP00000371994:T1172M	T	+	2	0	NYNRIN	23954310	0.518000	0.26234	0.997000	0.53966	0.945000	0.59286	0.655000	0.24933	2.379000	0.81126	0.561000	0.74099	ACG		0.657	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			
OR52I2	143502	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	4608985	4608985	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:4608985C>T	ENST00000312614.4	+	1	965	c.943C>T	c.(943-945)Cca>Tca	p.P315S		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P315S(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CGTGATCATCCCAGCCACCTT	0.512																																																	1	Substitution - Missense(1)	kidney(1)											204.0	191.0	195.0					11																	4608985		2201	4298	6499	SO:0001583	missense	143502			BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.943C>T	11.37:g.4608985C>T	ENSP00000308764:p.Pro315Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.823553	0.50739	.	.	ENSG00000226288	ENST00000312614	T	0.35048	1.33	4.18	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000459	T	0.57431	0.2053	M	0.81682	2.555	0.36355	D	0.860345	D	0.76494	0.999	D	0.69479	0.964	T	0.68172	-0.5479	10	0.87932	D	0	-5.5036	10.1938	0.43043	0.3609:0.6391:0.0:0.0	.	315	Q8NH67	O52I2_HUMAN	S	315	ENSP00000308764:P315S	ENSP00000308764:P315S	P	+	1	0	OR52I2	4565561	0.722000	0.28017	0.982000	0.44146	0.864000	0.49448	2.871000	0.48459	0.947000	0.37659	0.644000	0.83932	CCA		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1		NM_001005170	
OR4D5	219875	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	123810587	123810587	+	Silent	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:123810587C>T	ENST00000307033.2	+	1	338	c.264C>T	c.(262-264)ggC>ggT	p.G88G		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G88G(2)		autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGCTCTCAGGCAACCCTACCA	0.473																																																	2	Substitution - coding silent(2)	lung(1)|kidney(1)											158.0	130.0	140.0					11																	123810587		2202	4299	6501	SO:0001819	synonymous_variant	219875			BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"""GPCR / Class A : Olfactory receptors"""	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.264C>T	11.37:g.123810587C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B9EGZ4|Q6IFE6	Silent	SNP	ENST00000307033.2	37	CCDS31699.1																																																																																				0.473	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1		NM_001001965	
OTOP2	92736	broad.mit.edu;hgsc.bcm.edu	37	17	72920812	72920812	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr17:72920812C>G	ENST00000580223.1	+	1	115	c.85C>G	c.(85-87)Cgc>Ggc	p.R29G	USH1G_ENST00000319642.1_5'Flank|OTOP2_ENST00000331427.4_Missense_Mutation_p.R29G			Q7RTS6	OTOP2_HUMAN	otopetrin 2	29						integral component of membrane (GO:0016021)		p.R29G(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					GAAGGGTGGCCGCCTGCTGTC	0.706																																																	1	Substitution - Missense(1)	kidney(1)											20.0	17.0	18.0					17																	72920812		2194	4298	6492	SO:0001583	missense	92736			BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.85C>G	17.37:g.72920812C>G	ENSP00000463837:p.Arg29Gly	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000580223.1	37	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.567190	0.65651	.	.	ENSG00000183034	ENST00000331427	T	0.10860	2.83	3.99	3.99	0.46301	.	0.074165	0.64402	D	0.000020	T	0.28732	0.0712	L	0.58101	1.795	0.42411	D	0.992605	D	0.89917	1.0	D	0.70716	0.97	T	0.04811	-1.0925	10	0.56958	D	0.05	-6.7234	16.2671	0.82593	0.0:1.0:0.0:0.0	.	29	Q7RTS6	OTOP2_HUMAN	G	29	ENSP00000332528:R29G	ENSP00000332528:R29G	R	+	1	0	OTOP2	70432407	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	2.556000	0.45862	2.052000	0.61016	0.455000	0.32223	CGC		0.706	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1		NM_178160	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52584626	52584626	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:52584626G>A	ENST00000296302.7	-	29	4709	c.4708C>T	c.(4708-4710)Cag>Tag	p.Q1570*	PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Q1490*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Q1533*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Q1478*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Q1463*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Q1463*|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Q1483*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Q1515*|SMIM4_ENST00000476842.1_Intron			Q86U86	PB1_HUMAN	polybromo 1	1570	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Q1570*(1)|p.Q1463*(1)|p.Q1483*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GGTGGTGCCTGCTGCCCTGGA	0.557			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											76.0	79.0	78.0					3																	52584626		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4708C>T	3.37:g.52584626G>A	ENSP00000296302:p.Gln1570*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	44	10.635663	0.99441	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767	.	.	.	5.93	5.93	0.95920	.	0.060663	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-9.7937	20.3539	0.98825	0.0:0.0:1.0:0.0	.	.	.	.	X	1483;1463;1570;1463;1515;1490;1533;1478	.	ENSP00000296302:Q1570X	Q	-	1	0	PBRM1	52559666	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.912000	0.87465	2.826000	0.97356	0.655000	0.94253	CAG		0.557	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
JADE3	9767	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	46887437	46887437	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:46887437C>T	ENST00000218343.4	+	6	917	c.619C>T	c.(619-621)Cgg>Tgg	p.R207W	PHF16_ENST00000397189.1_Missense_Mutation_p.R207W	NM_014735.3	NP_055550.1												p.R207W(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						TGATGTGTGCCGGTCTCCAGA	0.468																																																	1	Substitution - Missense(1)	kidney(1)											355.0	227.0	271.0					X																	46887437		2203	4300	6503	SO:0001583	missense	9767																														ENST00000218343.4:c.619C>T	X.37:g.46887437C>T	ENSP00000218343:p.Arg207Trp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	C	33	5.229256	0.95173	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	D;D	0.88664	-2.41;-2.41	5.78	5.78	0.91487	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.049394	0.85682	D	0.000000	D	0.94951	0.8367	M	0.84326	2.69	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94781	0.7953	9	.	.	.	.	18.973	0.92722	0.0:1.0:0.0:0.0	.	207	Q92613	JADE3_HUMAN	W	207	ENSP00000380373:R207W;ENSP00000218343:R207W	.	R	+	1	2	PHF16	46772381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.713000	0.84693	2.428000	0.82296	0.594000	0.82650	CGG		0.468	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			
PKHD1L1	93035	broad.mit.edu;ucsc.edu	37	8	110432841	110432841	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr8:110432841G>A	ENST00000378402.5	+	23	2723	c.2619G>A	c.(2617-2619)atG>atA	p.M873I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	873					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.M875I(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GGCCAACTATGACAAACCAAT	0.383										HNSCC(38;0.096)																																							1	Substitution - Missense(1)	kidney(1)											140.0	130.0	133.0					8																	110432841		1850	4091	5941	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.2619G>A	8.37:g.110432841G>A	ENSP00000367655:p.Met873Ile	Somatic		WXS	Illumina GAIIx	Phase_I	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	0.153	-1.089018	0.01873	.	.	ENSG00000205038	ENST00000378402	D	0.84800	-1.9	5.54	-0.598	0.11649	.	0.812063	0.11345	N	0.573629	T	0.67748	0.2926	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49418	-0.8942	10	0.18710	T	0.47	.	1.2804	0.02040	0.3113:0.1421:0.4011:0.1456	.	873	Q86WI1	PKHL1_HUMAN	I	873	ENSP00000367655:M873I	ENSP00000367655:M873I	M	+	3	0	PKHD1L1	110502017	0.000000	0.05858	0.018000	0.16275	0.393000	0.30537	0.103000	0.15292	0.032000	0.15435	0.585000	0.79938	ATG		0.383	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1		NM_177531	
POSTN	10631	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	38162097	38162097	+	Silent	SNP	G	G	A	rs368300503		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr13:38162097G>A	ENST00000379747.4	-	5	585	c.468C>T	c.(466-468)aaC>aaT	p.N156N	POSTN_ENST00000379749.4_Silent_p.N156N|POSTN_ENST00000541481.1_Silent_p.N156N|POSTN_ENST00000379743.4_Silent_p.N156N|POSTN_ENST00000379742.4_Silent_p.N156N|POSTN_ENST00000541179.1_Silent_p.N156N	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	156	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)	p.N156N(2)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		CAACATTCACGTTGCTCTCCA	0.323																																																	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)						G	,,,	1,4405	2.1+/-5.4	0,1,2202	103.0	100.0	101.0		468,468,468,468	0.4	1.0	13		101	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	,,,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,,,	156/780,156/782,156/752,156/837	38162097	1,12995	2203	4295	6498	SO:0001819	synonymous_variant	10631			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.468C>T	13.37:g.38162097G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Silent	SNP	ENST00000379747.4	37	CCDS9364.1																																																																																				0.323	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2		NM_006475	
PRKRA	8575	hgsc.bcm.edu	37	2	179315735	179315736	+	Frame_Shift_Del	DEL	GC	GC	-	rs141354030|rs79769305	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:179315735_179315736delGC	ENST00000325748.4	-	1	222_223	c.22_23delGC	c.(22-24)gccfs	p.A8fs	PRKRA_ENST00000470200.1_5'UTR|DFNB59_ENST00000375129.4_5'Flank|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000487082.1_5'Flank|PRKRA_ENST00000438687.3_5'UTR|PRKRA_ENST00000432031.2_5'Flank	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	8	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CGGGGCCTCGGCGCGGTGCCTG	0.757														1193	0.238219	0.1649	0.3545	5008	,	,		12129	0.123		0.339	False		,,,				2504	0.2699				Melanoma(200;68 3001 23825 48764)												0										658,2174		225,208,983						-1.9	0.8		dbSNP_134	7	2206,4138		751,704,1717	no	frameshift	PRKRA	NM_003690.4		976,912,2700	A1A1,A1R,RR		34.773,23.2345,31.2119				2864,6312				SO:0001589	frameshift_variant	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.22_23delGC	2.37:g.179315737_179315738delGC	ENSP00000318176:p.Ala8fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	37	CCDS2279.1																																																																																				0.757	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2		NM_003690	
RBM14	10432	hgsc.bcm.edu	37	11	66392880	66392880	+	Silent	SNP	C	C	T	rs11550057	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:66392880C>T	ENST00000310137.4	+	2	1672	c.1533C>T	c.(1531-1533)acC>acT	p.T511T	RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000511114.1_Intron|RBM14-RBM4_ENST00000412278.2_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	511	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTTCTGCCACCCTGGCAGCTC	0.647													C|||	399	0.0796725	0.0136	0.0793	5008	,	,		15624	0.0208		0.1531	False		,,,				2504	0.1544																0								C	,,,,	155,4245	106.5+/-144.9	3,149,2048	50.0	46.0	47.0		,,,,1533	4.8	1.0	11	dbSNP_120	47	1377,7213	265.2+/-286.0	118,1141,3036	no	intron,intron,intron,intron,coding-synonymous	RBM14,RBM14-RBM4	NM_001198836.1,NM_001198837.1,NM_001198845.1,NM_001198846.1,NM_006328.3	,,,,	121,1290,5084	TT,TC,CC		16.0303,3.5227,11.7937	,,,,	,,,,511/670	66392880	1532,11458	2200	4295	6495	SO:0001819	synonymous_variant	10432			AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1533C>T	11.37:g.66392880C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	37	CCDS8147.1																																																																																				0.647	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1		NM_006328	
RHPN2	85415	hgsc.bcm.edu	37	19	33471129	33471129	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr19:33471129G>A	ENST00000254260.3	-	15	1869	c.1834C>T	c.(1834-1836)Cag>Tag	p.Q612*	RHPN2_ENST00000400226.4_Nonsense_Mutation_p.Q461*|RHPN2_ENST00000588683.1_5'UTR	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	612					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TACGTTTTCTGCATTCCCACG	0.413																																																	0													75.0	67.0	70.0					19																	33471129		2203	4297	6500	SO:0001587	stop_gained	85415			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1834C>T	19.37:g.33471129G>A	ENSP00000254260:p.Gln612*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Nonsense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	40	7.988834	0.98596	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	.	.	.	4.94	4.94	0.65067	.	0.169646	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-0.1256	18.5638	0.91110	0.0:0.0:1.0:0.0	.	.	.	.	X	612;342;461	.	ENSP00000254260:Q612X	Q	-	1	0	RHPN2	38162969	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.543000	0.82106	2.446000	0.82766	0.579000	0.79373	CAG		0.413	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2		NM_033103	
RIMBP3	85376	hgsc.bcm.edu	37	22	20460113	20460115	+	In_Frame_Del	DEL	CCG	CCG	-	rs201820173		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr22:20460113_20460115delCCG	ENST00000426804.1	-	1	1671_1673	c.1187_1189delCGG	c.(1186-1191)gcggag>gag	p.A396del		NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	396				A -> E (in Ref. 2; BAB33336). {ECO:0000305}.						breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			TGCTTGTTCTCCGCTTGCAGGGT	0.675																																																	0																																										SO:0001651	inframe_deletion	85376			AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.1187_1189delCGG	22.37:g.20460113_20460115delCCG	ENSP00000391564:p.Ala396del	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYP7|Q9BY94|Q9UFQ5	In_Frame_Del	DEL	ENST00000426804.1	37	CCDS46665.1																																																																																				0.675	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2		NM_015672	
RPS21	6227	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	60963416	60963419	+	Splice_Site	DEL	TCAA	TCAA	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	TCAA	TCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr20:60963416_60963419delTCAA	ENST00000343986.4	+	5	277_280	c.238_241delTCAA	c.(238-243)tcaaag>ag	p.SK80fs	RPS21_ENST00000370562.1_3'UTR|RPS21_ENST00000450116.2_Frame_Shift_Del_p.SK80fs|RPS21_ENST00000492356.2_3'UTR	NM_001024.3	NP_001015.1	P63220	RS21_HUMAN	ribosomal protein S21	80					cellular protein metabolic process (GO:0044267)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000461)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|structural constituent of ribosome (GO:0003735)			endometrium(2)|lung(1)|prostate(1)	4	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGGCATCGTCTCAAAGTAAGGTTG	0.485																																																	0																																										SO:0001630	splice_region_variant	6227			L04483	CCDS13497.1	20q13.3	2011-04-05			ENSG00000171858	ENSG00000171858		"""S ribosomal proteins"""	10409	protein-coding gene	gene with protein product	"""8.2 kDa differentiation factor"""	180477				8332502, 9582194	Standard	NM_001024		Approved	S21	uc002ycr.3	P63220	OTTHUMG00000032915	ENST00000343986.4:c.242+1TCAA>-	20.37:g.60963416_60963419delTCAA		Somatic		WXS	Illumina HiSeq	Phase_I	P35265	Frame_Shift_Del	DEL	ENST00000343986.4	37	CCDS13497.1																																																																																				0.485	RPS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080031.2		NM_001024	Frame_Shift_Del
S100PBP	64766	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	33292267	33292267	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:33292267T>G	ENST00000373475.5	+	3	821	c.567T>G	c.(565-567)aaT>aaG	p.N189K	S100PBP_ENST00000398243.3_Missense_Mutation_p.N189K|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000373476.1_Missense_Mutation_p.N189K	NM_022753.3	NP_073590.2			S100P binding protein									p.N189K(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTAGCCCAAATGAAAGCAAAC	0.443																																																	1	Substitution - Missense(1)	kidney(1)											71.0	76.0	75.0					1																	33292267		2203	4300	6503	SO:0001583	missense	64766			BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"""S100P binding protein 1"""	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.567T>G	1.37:g.33292267T>G	ENSP00000362574:p.Asn189Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000373475.5	37	CCDS30666.1	.	.	.	.	.	.	.	.	.	.	T	7.648	0.682369	0.14907	.	.	ENSG00000116497	ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689	.	.	.	5.32	1.79	0.24919	.	0.442058	0.24147	N	0.041117	T	0.24586	0.0596	L	0.32530	0.975	0.22903	N	0.99858	B;B	0.19583	0.001;0.037	B;B	0.19148	0.003;0.024	T	0.10019	-1.0648	8	.	.	.	-11.5554	3.2516	0.06816	0.1715:0.1801:0.0:0.6484	.	189;189	A8MTZ6;Q96BU1	.;S1PBP_HUMAN	K	189	.	.	N	+	3	2	S100PBP	33064854	0.920000	0.31207	0.935000	0.37517	0.156000	0.22039	0.244000	0.18124	0.543000	0.28864	0.533000	0.62120	AAT		0.443	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1		NM_022753	
S1PR4	8698	hgsc.bcm.edu	37	19	3179874	3179874	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr19:3179874C>T	ENST00000246115.3	+	1	1139	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C		NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	362					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						GGACAGCTTTCGCGGCTCCCG	0.672																																					GBM(82;318 1638 33279 49708)												0													48.0	58.0	55.0					19																	3179874		2177	4239	6416	SO:0001583	missense	8698			AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3170	protein-coding gene	gene with protein product		603751	"""endothelial differentiation, G-protein-coupled receptor 6"", ""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"""	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.1084C>T	19.37:g.3179874C>T	ENSP00000246115:p.Arg362Cys	Somatic		WXS	Illumina HiSeq	Phase_I	D6W612	Missense_Mutation	SNP	ENST00000246115.3	37	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396885	0.42512	.	.	ENSG00000125910	ENST00000246115	D	0.82255	-1.59	3.94	3.94	0.45596	.	0.699358	0.12803	N	0.437822	D	0.86377	0.5918	L	0.29908	0.895	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.86430	0.1760	10	0.72032	D	0.01	.	14.7234	0.69326	0.0:1.0:0.0:0.0	.	362	O95977	S1PR4_HUMAN	C	362	ENSP00000246115:R362C	ENSP00000246115:R362C	R	+	1	0	S1PR4	3130874	0.999000	0.42202	0.590000	0.28732	0.137000	0.21094	2.774000	0.47694	2.053000	0.61076	0.561000	0.74099	CGC		0.672	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1		NM_003775	
SAAL1	113174	hgsc.bcm.edu	37	11	18127558	18127559	+	In_Frame_Ins	INS	-	-	CGG	rs74589784|rs72431213|rs148650821	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr11:18127558_18127559insCGG	ENST00000524803.1	-	1	79_80	c.30_31insCCG	c.(28-33)ccgggt>ccgCCGggt	p.10_11insP	SAAL1_ENST00000529318.1_In_Frame_Ins_p.10_11insP|SAAL1_ENST00000533851.1_5'UTR|SAAL1_ENST00000300013.4_In_Frame_Ins_p.10_11insP			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	10				P -> PP (in Ref. 3; AAH12010). {ECO:0000305}.						breast(2)|large_intestine(5)|lung(8)	15						TTGTCGCGACCCGGCGGCGGCG	0.673											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		734	0.146565	0.0174	0.1556	5008	,	,		17393	0.1349		0.2604	False		,,,				2504	0.2096																0																																										SO:0001652	inframe_insertion	113174			AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.28_30dupCCG	11.37:g.18127565_18127567dupCGG	ENSP00000432487:p.Pro10_Pro10dup	Somatic	723	WXS	Illumina HiSeq	Phase_I	A6NH05	In_Frame_Ins	INS	ENST00000524803.1	37	CCDS31439.1																																																																																				0.673	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1		NM_138421	
SCAF1	58506	hgsc.bcm.edu	37	19	50154294	50154295	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr19:50154294_50154295insC	ENST00000360565.3	+	7	772_773	c.648_649insC	c.(649-651)cccfs	p.P217fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	217	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.A219fs*11(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CGCCCCCTGCACCCCCAGCCCC	0.688																																																	1	Insertion - Frameshift(1)	central_nervous_system(1)																																								SO:0001589	frameshift_variant	58506			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.653dupC	19.37:g.50154299_50154299dupC	ENSP00000353769:p.Pro217fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Ins	INS	ENST00000360565.3	37	CCDS33074.1																																																																																				0.688	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1		NM_021228	
SNTB1	6641	broad.mit.edu;hgsc.bcm.edu	37	8	121823811	121823811	+	Silent	SNP	G	G	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr8:121823811G>C	ENST00000395601.3	-	2	687	c.273C>G	c.(271-273)gtC>gtG	p.V91V	SNTB1_ENST00000519177.1_5'Flank|RP11-713M15.2_ENST00000605955.1_RNA|SNTB1_ENST00000517992.1_Silent_p.V91V	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	91	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)		p.V91V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			AAGCGGTGCGGAccccggcgg	0.741																																																	1	Substitution - coding silent(1)	kidney(1)											11.0	10.0	10.0					8																	121823811		2175	4256	6431	SO:0001819	synonymous_variant	6641			AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"""Pleckstrin homology (PH) domain containing"""	11168	protein-coding gene	gene with protein product	"""tax interaction protein 43"""	600026	"""syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"""	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.273C>G	8.37:g.121823811G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K9E0|O14912|Q4KMG8	Silent	SNP	ENST00000395601.3	37	CCDS6334.1																																																																																				0.741	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1		NM_021021	
SPTBN5	51332	broad.mit.edu;hgsc.bcm.edu	37	15	42150817	42150817	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr15:42150817G>C	ENST00000320955.6	-	49	8436	c.8209C>G	c.(8209-8211)Cag>Gag	p.Q2737E		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2737					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.Q2737E(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AGCTCCTGCTGTTGGTGCATG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											23.0	25.0	24.0					15																	42150817		2164	4270	6434	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8209C>G	15.37:g.42150817G>C	ENSP00000317790:p.Gln2737Glu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	10.24	1.294564	0.23564	.	.	ENSG00000137877	ENST00000320955	T	0.50001	0.76	4.27	3.35	0.38373	.	0.722220	0.11747	N	0.533424	T	0.45276	0.1334	L	0.57536	1.79	0.09310	N	1	P	0.38280	0.625	B	0.34931	0.192	T	0.34825	-0.9813	10	0.59425	D	0.04	.	13.2627	0.60115	0.0:0.182:0.818:0.0	.	2737	Q9NRC6	SPTN5_HUMAN	E	2737	ENSP00000317790:Q2737E	ENSP00000317790:Q2737E	Q	-	1	0	SPTBN5	39938109	0.001000	0.12720	0.001000	0.08648	0.172000	0.22775	0.595000	0.24029	0.985000	0.38656	0.467000	0.42956	CAG		0.627	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1		NM_016642	
SUCLG1	8802	broad.mit.edu;ucsc.edu	37	2	84652703	84652703	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr2:84652703A>C	ENST00000393868.2	-	8	1060	c.850T>G	c.(850-852)Tcc>Gcc	p.S284A	SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	284					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)	p.S284A(1)		kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	GCAATGAAGGACACTACAGGC	0.433																																					Ovarian(48;203 1101 37206 40305 50790)												1	Substitution - Missense(1)	kidney(1)											125.0	135.0	132.0					2																	84652703		2203	4300	6503	SO:0001583	missense	8802			Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"""succinate-CoA ligase, GDP-forming, alpha subunit"""			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.850T>G	2.37:g.84652703A>C	ENSP00000377446:p.Ser284Ala	Somatic		WXS	Illumina GAIIx	Phase_I	Q9BWB0|Q9UNP6	Missense_Mutation	SNP	ENST00000393868.2	37	CCDS1967.2	.	.	.	.	.	.	.	.	.	.	A	16.53	3.147871	0.57151	.	.	ENSG00000163541	ENST00000393868	T	0.65916	-0.18	6.16	6.16	0.99307	Succinyl-CoA synthetase-like (2);ATP-citrate lyase/succinyl-CoA ligase (1);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	N	0.12182	0.205	0.80722	D	1	B	0.13145	0.007	B	0.30251	0.113	T	0.42865	-0.9426	10	0.27785	T	0.31	-16.6422	14.7581	0.69583	1.0:0.0:0.0:0.0	.	284	P53597	SUCA_HUMAN	A	284	ENSP00000377446:S284A	ENSP00000377446:S284A	S	-	1	0	SUCLG1	84506214	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TCC		0.433	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2		NM_003849	
TGIF2LX	90316	broad.mit.edu;hgsc.bcm.edu	37	X	89177557	89177557	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:89177557C>A	ENST00000561129.2	+	1	603	c.473C>A	c.(472-474)cCc>cAc	p.P158H	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.P158H			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P158H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						CAAAGCCTGCCCCTGTGGCCC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											44.0	46.0	45.0					X																	89177557		2203	4300	6503	SO:0001583	missense	90316			AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"""Homeoboxes / TALE class"""	18570	protein-coding gene	gene with protein product		300411	"""TGFB-induced factor 2-like, X-linked"""				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.473C>A	X.37:g.89177557C>A	ENSP00000453704:p.Pro158His	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	37	CCDS14459.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.831676	0.32421	.	.	ENSG00000153779	ENST00000283891	T	0.66815	-0.23	2.38	0.433	0.16534	.	2.322460	0.02478	N	0.088187	T	0.76962	0.4061	M	0.63843	1.955	0.09310	N	1	D	0.89917	1.0	D	0.68765	0.96	T	0.53968	-0.8363	9	.	.	.	-4.6386	3.8679	0.09024	0.2368:0.6094:0.0:0.1538	.	158	Q8IUE1	TF2LX_HUMAN	H	158	ENSP00000355119:P158H	.	P	+	2	0	TGIF2LX	89064213	0.003000	0.15002	0.000000	0.03702	0.012000	0.07955	1.352000	0.34033	0.009000	0.14813	0.506000	0.49869	CCC		0.602	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2		NM_138960	
TBC1D8B	54885	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	106093257	106093257	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:106093257G>A	ENST00000357242.5	+	12	2014	c.1840G>A	c.(1840-1842)Gcc>Acc	p.A614T	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.A608T	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	614	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.A614T(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TTCTGTAGGTGCCTTGGTGGA	0.383																																																	1	Substitution - Missense(1)	kidney(1)											138.0	114.0	122.0					X																	106093257		2203	4300	6503	SO:0001583	missense	54885			AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.1840G>A	X.37:g.106093257G>A	ENSP00000349781:p.Ala614Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	37	CCDS14522.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.696674	0.88830	.	.	ENSG00000133138	ENST00000357242;ENST00000276175	T;T	0.21734	1.99;1.99	4.76	4.76	0.60689	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.43809	0.1264	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.23404	-1.0189	10	0.29301	T	0.29	-6.6176	15.6789	0.77352	0.0:0.0:1.0:0.0	.	614	Q0IIM8	TBC8B_HUMAN	T	614;608	ENSP00000349781:A614T;ENSP00000276175:A608T	ENSP00000276175:A608T	A	+	1	0	TBC1D8B	105979913	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	9.813000	0.99286	2.082000	0.62665	0.594000	0.82650	GCC		0.383	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2		NM_017752	
TAZ	6901	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	153649068	153649068	+	Missense_Mutation	SNP	G	G	T	rs368990588		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:153649068G>T	ENST00000350743.4	+	9	970	c.681G>T	c.(679-681)aaG>aaT	p.K227N	TAZ_ENST00000369776.4_Missense_Mutation_p.K227N|TAZ_ENST00000351413.4_Missense_Mutation_p.K243N|TAZ_ENST00000369790.4_Missense_Mutation_p.K213N|TAZ_ENST00000498029.1_3'UTR|TAZ_ENST00000299328.5_Missense_Mutation_p.K257N|TAZ_ENST00000475699.1_Missense_Mutation_p.K230N	NM_181311.2	NP_851828.1	Q9GZV5	WWTR1_HUMAN	tafazzin	0	Gln-rich.				cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.K257N(1)		lung(1)	1	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGGAGAACAAGTCGGCTGTGA	0.647																																																	1	Substitution - Missense(1)	kidney(1)											67.0	62.0	64.0					X																	153649068		2203	4300	6503	SO:0001583	missense	6901			X92762	CCDS14748.1, CCDS14749.1, CCDS14750.1, CCDS35450.1	Xq28	2014-09-17	2008-07-29		ENSG00000102125	ENSG00000102125			11577	protein-coding gene	gene with protein product	"""Barth syndrome"""	300394	"""endocardial fibroelastosis 2"", ""cardiomyopathy, dilated 3A (X-linked)"""	CMD3A, EFE2, EFE		8042670	Standard	NM_000116		Approved	BTHS, XAP-2, G4.5	uc004fkx.3	Q16635	OTTHUMG00000033190	ENST00000350743.4:c.681G>T	X.37:g.153649068G>T	ENSP00000338891:p.Lys227Asn	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000350743.4	37	CCDS14749.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.115934	0.37339	.	.	ENSG00000102125	ENST00000369790;ENST00000299328;ENST00000350743;ENST00000351413;ENST00000369776;ENST00000475699	D;D;D;D;D;D	0.98531	-3.25;-3.25;-3.25;-3.25;-4.98;-3.25	4.79	3.02	0.34903	.	0.183845	0.46145	D	0.000306	D	0.96648	0.8906	L	0.57536	1.79	0.31414	N	0.675073	P;P;B;P;P;D	0.53619	0.823;0.615;0.441;0.687;0.745;0.961	P;B;B;B;P;P	0.49637	0.459;0.28;0.238;0.398;0.568;0.617	D	0.93515	0.6856	10	0.18710	T	0.47	-7.3388	6.678	0.23106	0.3095:0.0:0.6905:0.0	.	261;227;213;227;243;257	A6XNE1;Q96F92;Q16635-7;Q16635-3;Q16635-5;Q16635	.;.;.;.;.;TAZ_HUMAN	N	213;257;227;243;227;230	ENSP00000358805:K213N;ENSP00000299328:K257N;ENSP00000338891:K227N;ENSP00000218246:K243N;ENSP00000358791:K227N;ENSP00000419854:K230N	ENSP00000299328:K257N	K	+	3	2	TAZ	153302262	1.000000	0.71417	0.800000	0.32199	0.286000	0.27126	0.963000	0.29293	0.320000	0.23234	0.525000	0.51046	AAG		0.647	TAZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080939.1			
TP53BP2	7159	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	223983623	223983623	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr1:223983623G>A	ENST00000343537.7	-	13	2909	c.2618C>T	c.(2617-2619)cCt>cTt	p.P873L	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Missense_Mutation_p.P106L|TP53BP2_ENST00000391878.2_Missense_Mutation_p.P744L	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	867	Pro-rich.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.P744L(1)|p.P873L(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		TGGGTATGGAGGGTACTCCTC	0.582																																																	2	Substitution - Missense(2)	kidney(2)											94.0	97.0	96.0					1																	223983623		2203	4300	6503	SO:0001583	missense	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2618C>T	1.37:g.223983623G>A	ENSP00000341957:p.Pro873Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.756323	0.89843	.	.	ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879	T;T;T	0.53206	0.74;0.92;0.63	5.55	5.55	0.83447	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.70307	0.3209	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.69300	-0.5181	10	0.44086	T	0.13	.	19.5118	0.95144	0.0:0.0:1.0:0.0	.	873;867	B4DG66;Q13625	.;ASPP2_HUMAN	L	744;873;106	ENSP00000375750:P744L;ENSP00000341957:P873L;ENSP00000375751:P106L	ENSP00000341957:P873L	P	-	2	0	TP53BP2	222050246	1.000000	0.71417	0.993000	0.49108	0.808000	0.45660	9.230000	0.95299	2.634000	0.89283	0.563000	0.77884	CCT		0.582	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3		NM_001031685, NM_005426	
TRIOBP	11078	hgsc.bcm.edu;ucsc.edu	37	22	38109337	38109337	+	Silent	SNP	C	C	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr22:38109337C>T	ENST00000406386.3	+	5	630	c.375C>T	c.(373-375)agC>agT	p.S125S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	125					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TGTGTGGCAGCTGCAACGAGG	0.647																																																	0													86.0	104.0	98.0					22																	38109337		2113	4247	6360	SO:0001819	synonymous_variant	11078			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.375C>T	22.37:g.38109337C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																				0.647	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			
SMG1P7	100506060	broad.mit.edu	37	16	70268121	70268121	+	RNA	SNP	C	C	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr16:70268121C>G	ENST00000459379.1	-	0	0																											AGACGGAAGACAGAATAAAGG	0.338																																																	0																																												0																															16.37:g.70268121C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.338	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
ROCK1P1	727758	broad.mit.edu	37	18	109344	109344	+	RNA	SNP	T	T	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr18:109344T>A	ENST00000608049.1	+	0	280					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		aggctttgcctacaggggaca	0.483																																																	0																																												0					18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.109344T>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000608049.1	37																																																																																					0.483	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			
ROCK1P1	727758	broad.mit.edu	37	18	109348	109348	+	RNA	SNP	G	G	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr18:109348G>A	ENST00000608049.1	+	0	284					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		tttgcctacaggggacattgt	0.478																																																	0																																												0					18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.109348G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000608049.1	37																																																																																					0.478	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			
MARCH6	10299	broad.mit.edu	37	5	10437892	10437892	+	3'UTR	DEL	T	T	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr5:10437892delT	ENST00000274140.5	+	0	6961				MARCH6_ENST00000606497.1_3'UTR	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase						protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						AAATGCTCCCTTTTTAATGTG	0.328																																																	0																																										SO:0001624	3_prime_UTR_variant	0			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.*4096T>-	5.37:g.10437892delT		Somatic		WXS	Illumina GAIIx	Phase_I	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	RNA	DEL	ENST00000274140.5	37	CCDS34135.1																																																																																				0.328	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2		NM_005885	
WASH6P	653440	broad.mit.edu	37	X	155252868	155252868	+	RNA	SNP	T	T	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chrX:155252868T>A	ENST00000461007.1	+	0	1876				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.P304P(5)									TAGCCGAGCCTCTCAAGGCAG	0.632																																																	5	Substitution - coding silent(5)	kidney(3)|endometrium(2)																																										0			AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155252868T>A		Somatic		WXS	Illumina GAIIx	Phase_I	A6NGF1|Q8N305	Silent	SNP	ENST00000461007.1	37																																																																																					0.632	WASH6P-016	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000058840.1		NG_008380	
USP7	7874	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	9012898	9012898	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr16:9012898T>G	ENST00000344836.4	-	6	908	c.710A>C	c.(709-711)cAg>cCg	p.Q237P	USP7_ENST00000381886.4_Missense_Mutation_p.Q221P|USP7_ENST00000535863.1_Missense_Mutation_p.Q138P	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	237	USP.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Q237P(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CTTTCGTAGCTGATTCGTGAA	0.468																																																	1	Substitution - Missense(1)	kidney(1)											197.0	167.0	178.0					16																	9012898		2197	4300	6497	SO:0001583	missense	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.710A>C	16.37:g.9012898T>G	ENSP00000343535:p.Gln237Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6NMY8|B7Z815|H0Y3G8	Missense_Mutation	SNP	ENST00000344836.4	37	CCDS32385.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.567048	0.45694	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	T;T;T;T	0.32988	1.55;1.43;1.55;1.55	5.69	5.69	0.88448	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.34106	0.0886	N	0.10664	0.02	0.80722	D	1	D;D	0.69078	0.987;0.997	D;D	0.68192	0.956;0.956	T	0.33471	-0.9867	10	0.29301	T	0.29	.	15.9537	0.79865	0.0:0.0:0.0:1.0	.	237;221	Q93009;B7Z815	UBP7_HUMAN;.	P	237;245;138;138;179	ENSP00000343535:Q237P;ENSP00000371310:Q245P;ENSP00000443646:Q138P;ENSP00000439272:Q179P	ENSP00000343535:Q237P	Q	-	2	0	USP7	8920399	1.000000	0.71417	0.783000	0.31826	0.548000	0.35241	7.921000	0.87530	2.179000	0.69175	0.528000	0.53228	CAG		0.468	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			
VHL	7428	hgsc.bcm.edu	37	3	10183646	10183646	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4164-01A-02W-1382-10	TCGA-BP-4164-11A-01W-1244-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	94a19895-3cda-423b-a794-6944be76cc68	61b19171-22fd-4ca7-ba5b-fc15b0003fd2	g.chr3:10183646G>A	ENST00000256474.2	+	1	955	c.115G>A	c.(115-117)Ggc>Agc	p.G39S	VHL_ENST00000345392.2_Missense_Mutation_p.G39S|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	39	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.G39S(2)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CGAGGAGTCCGGCCCGGAAGA	0.736		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	2	Substitution - Missense(2)	kidney(2)											6.0	9.0	8.0					3																	10183646		1998	3901	5899	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.115G>A	3.37:g.10183646G>A	ENSP00000256474:p.Gly39Ser	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827744	0.50845	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.85773	-2.03;-2.03	3.71	-0.384	0.12474	.	0.363857	0.24742	N	0.035963	T	0.66470	0.2792	N	0.19112	0.55	0.09310	N	1	B;B	0.20780	0.048;0.013	B;B	0.11329	0.006;0.002	T	0.51244	-0.8730	10	0.35671	T	0.21	-1.8965	1.3303	0.02133	0.2144:0.3545:0.274:0.1571	.	39;39	P40337-2;P40337	.;VHL_HUMAN	S	39	ENSP00000256474:G39S;ENSP00000344757:G39S	ENSP00000256474:G39S	G	+	1	0	VHL	10158646	0.001000	0.12720	0.000000	0.03702	0.046000	0.14306	0.486000	0.22340	-0.085000	0.12573	0.555000	0.69702	GGC		0.736	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10183650	10183650	+	Missense_Mutation	SNP	C	C	T	rs200343185	byFrequency	TCGA-BP-4164-01A-02W-1382-10	TCGA-BP-4164-11A-01W-1244-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	94a19895-3cda-423b-a794-6944be76cc68	61b19171-22fd-4ca7-ba5b-fc15b0003fd2	g.chr3:10183650C>T	ENST00000256474.2	+	1	959	c.119C>T	c.(118-120)cCg>cTg	p.P40L	VHL_ENST00000345392.2_Missense_Mutation_p.P40L|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	40	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)			adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAGTCCGGCCCGGAAGAGTCC	0.736		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia				C|||	5	0.000998403	0.0	0.0	5008	,	,		10256	0.001		0.001	False		,,,				2504	0.0031					.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	0													6.0	9.0	8.0					3																	10183650		2021	3931	5952	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.119C>T	3.37:g.10183650C>T	ENSP00000256474:p.Pro40Leu	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	1	0.0017482517482517483	0	0.0	C	16.34	3.094509	0.56075	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.85171	-1.95;-1.95	3.6	3.6	0.41247	.	0.340736	0.26328	N	0.025001	T	0.67942	0.2947	N	0.19112	0.55	0.09310	N	1	P;P	0.42871	0.792;0.495	B;B	0.28305	0.088;0.027	T	0.67197	-0.5731	10	0.87932	D	0	-1.1666	8.6456	0.34003	0.2279:0.7721:0.0:0.0	.	40;40	P40337-2;P40337	.;VHL_HUMAN	L	40	ENSP00000256474:P40L;ENSP00000344757:P40L	ENSP00000256474:P40L	P	+	2	0	VHL	10158650	0.000000	0.05858	0.009000	0.14445	0.065000	0.16274	-0.034000	0.12225	2.318000	0.78349	0.555000	0.69702	CCG		0.736	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10183653	10183653	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4164-01A-02W-1382-10	TCGA-BP-4164-11A-01W-1244-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	94a19895-3cda-423b-a794-6944be76cc68	61b19171-22fd-4ca7-ba5b-fc15b0003fd2	g.chr3:10183653A>G	ENST00000256474.2	+	1	962	c.122A>G	c.(121-123)gAa>gGa	p.E41G	VHL_ENST00000345392.2_Missense_Mutation_p.E41G|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	41	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.E41V(2)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TCCGGCCCGGAAGAGTCCGGC	0.741		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	2	Substitution - Missense(2)	kidney(2)											6.0	9.0	8.0					3																	10183653		2033	3967	6000	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.122A>G	3.37:g.10183653A>G	ENSP00000256474:p.Glu41Gly	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.074053	0.55646	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.81996	-1.56;-1.56	3.51	-0.255	0.12988	.	0.388567	0.18780	N	0.131372	T	0.65165	0.2665	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.0	T	0.54761	-0.8245	10	0.72032	D	0.01	-0.9626	2.9359	0.05815	0.4622:0.0:0.3389:0.1988	.	41;41	P40337-2;P40337	.;VHL_HUMAN	G	41	ENSP00000256474:E41G;ENSP00000344757:E41G	ENSP00000256474:E41G	E	+	2	0	VHL	10158653	0.000000	0.05858	0.008000	0.14137	0.070000	0.16714	-0.836000	0.04382	-0.037000	0.13646	0.397000	0.26171	GAA		0.741	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10183659	10183659	+	Missense_Mutation	SNP	C	C	T	rs202164771		TCGA-BP-4164-01A-02W-1382-10	TCGA-BP-4164-11A-01W-1244-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PacBio	.		Illumina GAIIx	94a19895-3cda-423b-a794-6944be76cc68	61b19171-22fd-4ca7-ba5b-fc15b0003fd2	g.chr3:10183659C>T	ENST00000256474.2	+	1	968	c.128C>T	c.(127-129)tCc>tTc	p.S43F	VHL_ENST00000345392.2_Missense_Mutation_p.S43F|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	43	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)			adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCGGAAGAGTCCGGCCCGGAG	0.731		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	0													6.0	9.0	8.0					3																	10183659		2051	4000	6051	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.128C>T	3.37:g.10183659C>T	ENSP00000256474:p.Ser43Phe	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	9.166	1.019898	0.19355	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.84873	-1.91;-1.91	2.91	0.996	0.19844	.	1.235560	0.06248	N	0.691590	T	0.74794	0.3763	N	0.19112	0.55	0.09310	N	1	P;B	0.39782	0.688;0.139	B;B	0.34242	0.178;0.037	T	0.63844	-0.6545	10	0.62326	D	0.03	-3.9402	10.7123	0.45990	0.0:0.4032:0.5968:0.0	.	43;43	P40337-2;P40337	.;VHL_HUMAN	F	43	ENSP00000256474:S43F;ENSP00000344757:S43F	ENSP00000256474:S43F	S	+	2	0	VHL	10158659	0.003000	0.15002	0.013000	0.15412	0.035000	0.12851	0.175000	0.16762	0.260000	0.21731	0.555000	0.69702	TCC		0.731	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10183665	10183665	+	Missense_Mutation	SNP	C	C	T	rs199583685		TCGA-BP-4164-01A-02W-1382-10	TCGA-BP-4164-11A-01W-1244-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	94a19895-3cda-423b-a794-6944be76cc68	61b19171-22fd-4ca7-ba5b-fc15b0003fd2	g.chr3:10183665C>T	ENST00000256474.2	+	1	974	c.134C>T	c.(133-135)cCg>cTg	p.P45L	VHL_ENST00000345392.2_Missense_Mutation_p.P45L|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	45	8 X 5 AA tandem repeats of G-[PAVG]-E-E- [DAYSLE].				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)			adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAGTCCGGCCCGGAGGAACTG	0.716		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia				C|||	1	0.000199681	0.0	0.0	5008	,	,		10527	0.001		0.0	False		,,,				2504	0.0					.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	0																																										SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.134C>T	3.37:g.10183665C>T	ENSP00000256474:p.Pro45Leu	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	14.59	2.580733	0.46006	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.84298	-1.83;-1.83	3.53	0.582	0.17412	.	1.482540	0.04888	N	0.448902	T	0.73737	0.3625	N	0.19112	0.55	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.19666	0.026;0.012	T	0.61192	-0.7112	10	0.72032	D	0.01	0.0061	2.9019	0.05708	0.1708:0.3546:0.3717:0.1029	.	45;45	P40337-2;P40337	.;VHL_HUMAN	L	45	ENSP00000256474:P45L;ENSP00000344757:P45L	ENSP00000256474:P45L	P	+	2	0	VHL	10158665	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.435000	0.21510	0.107000	0.17824	0.555000	0.69702	CCG		0.716	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	broad.mit.edu;hgsc.bcm.edu	37	3	10191532	10191532	+	Nonsense_Mutation	SNP	C	C	A	rs5030835		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	feb8c145-040a-40c0-96f6-a2b389073dd9	8eb5b726-ce04-4244-a453-0dfa12704f79	g.chr3:10191532C>A	ENST00000256474.2	+	3	1365	c.525C>A	c.(523-525)taC>taA	p.Y175*	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Nonsense_Mutation_p.Y134*	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	175			Y -> D (in VHLD; type I). {ECO:0000269|PubMed:9829911}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.Y175*(5)|p.P172fs*39(2)|p.Y175fs*1(1)|p.Y175_L178>*(1)|p.R176fs*36(1)|p.E173fs*26(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CTGAGAATTACAGGAGACTGG	0.527		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	11	Substitution - Nonsense(5)|Deletion - Frameshift(5)|Complex - deletion inframe(1)	kidney(11)	GRCh37	CD071418|CM024001|CM961437	VHL	D|M	rs5030835						92.0	83.0	86.0					3																	10191532		2203	4300	6503	SO:0001587	stop_gained	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.525C>A	3.37:g.10191532C>A	ENSP00000256474:p.Tyr175*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Nonsense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040474	0.75732	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	.	.	.	4.97	1.89	0.25635	.	0.137522	0.50627	D	0.000109	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6215	9.5045	0.39037	0.0:0.7609:0.0:0.2391	.	.	.	.	X	175;134;93	.	ENSP00000256474:Y175X	Y	+	3	2	VHL	10166532	0.856000	0.29760	0.916000	0.36221	0.974000	0.67602	0.518000	0.22847	0.270000	0.21984	0.655000	0.94253	TAC		0.527	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
