#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ACTR3C	653857	broad.mit.edu	37	7	149990455	149990455	+	Silent	SNP	T	T	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr7:149990455T>C	ENST00000539352.1	-	3	350	c.99A>G	c.(97-99)acA>acG	p.T33T	ACTR3C_ENST00000252071.4_Silent_p.T33T	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	33						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.T33T(1)									TCCCCGTTAATGTACGTTCAC	0.468																																																	1	Substitution - coding silent(1)	kidney(1)											165.0	135.0	144.0					7																	149990455		692	1591	2283	SO:0001819	synonymous_variant	653857				CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.99A>G	7.37:g.149990455T>C			Q5CZI4	Silent	SNP	ENST00000539352.1	37	CCDS47744.1																																																																																				0.468	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2			
KIAA0226L	80183	broad.mit.edu;hgsc.bcm.edu	37	13	46935677	46935677	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr13:46935677C>G	ENST00000429979.1	-	8	1622	c.1018G>C	c.(1018-1020)Gaa>Caa	p.E340Q	KIAA0226L_ENST00000378787.3_Missense_Mutation_p.E340Q|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.E183Q|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.E183Q|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.E340Q|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.E205Q|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.E273Q|KIAA0226L_ENST00000378797.2_Missense_Mutation_p.E340Q|KIAA0226L_ENST00000378781.3_Missense_Mutation_p.Q319H	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	340								p.E340Q(1)		NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GCTAATAGTTCTGCAGAATTG	0.453																																																	1	Substitution - Missense(1)	kidney(1)											67.0	60.0	62.0					13																	46935677		2203	4300	6503	SO:0001583	missense	0			AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1018G>C	13.37:g.46935677C>G	ENSP00000396935:p.Glu340Gln		A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.17|19.17	3.775408|3.775408	0.70107|0.70107	.|.	.|.	ENSG00000102445|ENSG00000102445	ENST00000429979;ENST00000378797;ENST00000378784;ENST00000389908;ENST00000378787;ENST00000409879;ENST00000322896;ENST00000534925|ENST00000378781	T;T;T;T;T;T|T	0.58358|0.47177	0.44;0.34;0.49;0.44;0.34;0.54|0.85	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.078284|.	0.53938|.	D|.	0.000047|.	T|T	0.62134|0.62134	0.2403|0.2403	M|M	0.66939|0.66939	2.045|2.045	0.25627|0.25627	N|N	0.986349|0.986349	D;D;D;D;D;D|.	0.89917|.	0.994;0.998;0.999;0.998;1.0;1.0|.	P;P;P;P;D;D|.	0.74023|.	0.767;0.842;0.879;0.879;0.967;0.982|.	T|T	0.58346|0.58346	-0.7652|-0.7652	10|7	0.66056|0.87932	D|D	0.02|0	-9.9685|-9.9685	16.9164|16.9164	0.86153|0.86153	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	183;183;340;205;273;340|.	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3;Q9H714-4|.	.;.;K226L_HUMAN;.;.;.|.	Q|H	340;340;273;340;340;183;183;205|319	ENSP00000396935:E340Q;ENSP00000368074:E340Q;ENSP00000368061:E273Q;ENSP00000374558:E340Q;ENSP00000368064:E340Q;ENSP00000437501:E205Q|ENSP00000368057:Q319H	ENSP00000315633:E183Q|ENSP00000368057:Q319H	E|Q	-|-	1|3	0|2	KIAA0226L|KIAA0226L	45833678|45833678	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.611000|0.611000	0.37282|0.37282	3.064000|3.064000	0.49986|0.49986	2.743000|2.743000	0.94032|0.94032	0.643000|0.643000	0.83706|0.83706	GAA|CAG		0.453	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2		NM_025113	
ANKRD30BP2	149992	broad.mit.edu	37	21	14417489	14417489	+	RNA	SNP	C	C	G	rs373809076		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr21:14417489C>G	ENST00000507941.1	+	0	101				RNU6-614P_ENST00000384369.1_RNA					ankyrin repeat domain 30B pseudogene 2																		TACAGGCTGGCCACACACCAC	0.299																																																	0																																												0			AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309			16620	pseudogene	pseudogene	"""cancer/testis antigen 85"""		"""chromosome 21 open reading frame 99"""	C21orf99		12036297, 17114284	Standard	NR_026916		Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164		21.37:g.14417489C>G				RNA	SNP	ENST00000507941.1	37																																																																																					0.299	ANKRD30BP2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000372094.1		NR_026916	
BRAT1	221927	broad.mit.edu	37	7	2577862	2577862	+	Silent	SNP	A	A	G			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr7:2577862A>G	ENST00000340611.4	-	14	2563	c.2307T>C	c.(2305-2307)ccT>ccC	p.P769P	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	769					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)		p.P769P(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GCACAGCCTCAGGCTCCTGGT	0.716																																																	1	Substitution - coding silent(1)	kidney(1)											17.0	19.0	18.0					7																	2577862		2198	4286	6484	SO:0001819	synonymous_variant	0			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.2307T>C	7.37:g.2577862A>G			A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																				0.716	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2		NM_152743	
CHD4	1108	hgsc.bcm.edu	37	12	6711145	6711147	+	In_Frame_Del	DEL	TCC	TCC	-	rs71584865|rs1639122	byFrequency	TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr12:6711145_6711147delTCC	ENST00000357008.2	-	4	580_582	c.417_419delGGA	c.(415-420)gaggat>gat	p.E139del	CHD4_ENST00000544484.1_In_Frame_Del_p.E136del|CHD4_ENST00000309577.6_In_Frame_Del_p.E139del|CHD4_ENST00000544040.1_In_Frame_Del_p.E132del	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	139	Poly-Asp.		E -> D (in dbSNP:rs1639122). {ECO:0000269|PubMed:7575689}.		ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						ATCATCATCAtcctcctcctcct	0.453																																					Colon(32;586 792 4568 16848 45314)												0																																										SO:0001651	inframe_deletion	1108			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.417_419delGGA	12.37:g.6711154_6711156delTCC	ENSP00000349508:p.Glu139del		Q8IXZ5	In_Frame_Del	DEL	ENST00000357008.2	37	CCDS8552.1																																																																																				0.453	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001273	
CHIA	27159	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	111860638	111860638	+	Silent	SNP	C	C	T	rs148384495		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr1:111860638C>T	ENST00000369740.1	+	8	739	c.636C>T	c.(634-636)taC>taT	p.Y212Y	CHIA_ENST00000343320.6_Silent_p.Y212Y|CHIA_ENST00000483391.1_Silent_p.Y51Y|CHIA_ENST00000353665.6_Silent_p.Y51Y|CHIA_ENST00000430615.1_Silent_p.Y104Y|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000451398.2_Silent_p.Y51Y	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	212	Chitooligosaccharide binding. {ECO:0000305}.				apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)	p.Y212Y(1)|p.Y104Y(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCATGACCTACGACCTCCATG	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		20287	0.0		0.0	False		,,,				2504	0.001																2	Substitution - coding silent(2)	kidney(2)						C	,	1,4405	2.1+/-5.4	0,1,2202	96.0	89.0	91.0		312,636	-0.7	0.9	1	dbSNP_134	91	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	CHIA	NM_021797.2,NM_201653.2	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	104/369,212/477	111860638	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	27159			AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.636C>T	1.37:g.111860638C>T			Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																				0.542	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			
CKAP5	9793	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	46782199	46782199	+	Missense_Mutation	SNP	G	G	A	rs540835227		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr11:46782199G>A	ENST00000529230.1	-	33	4403	c.4357C>T	c.(4357-4359)Cgc>Tgc	p.R1453C	CKAP5_ENST00000415402.1_Missense_Mutation_p.R1453C|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1453C|SNORD67_ENST00000516618.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1453C|SNORD67_ENST00000390833.1_RNA			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1453					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)		p.R1453C(1)		breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						GGTCCCTTGCGTAACATGTTG	0.483													G|||	1	0.000199681	0.0	0.0	5008	,	,		20329	0.001		0.0	False		,,,				2504	0.0				Ovarian(4;85 273 2202 4844 13323)												1	Substitution - Missense(1)	kidney(1)											239.0	197.0	211.0					11																	46782199		2201	4299	6500	SO:0001583	missense	9793				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.4357C>T	11.37:g.46782199G>A	ENSP00000432768:p.Arg1453Cys		Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.036557|4.036557	0.75617|0.75617	.|.	.|.	ENSG00000175216|ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876|ENST00000527333	T;T;T;T|.	0.51071|.	0.72;0.74;0.74;0.74|.	6.03|6.03	5.12|5.12	0.69794|0.69794	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56455|0.56455	0.1986|0.1986	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	D;B;B|.	0.89917|.	1.0;0.004;0.002|.	D;B;B|.	0.72625|.	0.978;0.001;0.0|.	T|T	0.52866|0.52866	-0.8518|-0.8518	10|5	0.59425|.	D|.	0.04|.	-10.0088|-10.0088	15.5956|15.5956	0.76578|0.76578	0.0658:0.0:0.9342:0.0|0.0658:0.0:0.9342:0.0	.|.	1453;1453;1453|.	Q14008-3;Q14008-2;Q14008|.	.;.;CKAP5_HUMAN|.	C|M	1453;1453;1453;1453;176|1	ENSP00000432768:R1453C;ENSP00000395302:R1453C;ENSP00000310227:R1453C;ENSP00000346566:R1453C|.	ENSP00000310227:R1453C|.	R|T	-|-	1|2	0|0	CKAP5|CKAP5	46738775|46738775	1.000000|1.000000	0.71417|0.71417	0.939000|0.939000	0.37840|0.37840	0.997000|0.997000	0.91878|0.91878	5.506000|5.506000	0.66993|0.66993	1.556000|1.556000	0.49512|0.49512	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.483	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1		NM_014756	
COL6A3	1293	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	238249678	238249678	+	Silent	SNP	A	A	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr2:238249678A>C	ENST00000295550.4	-	38	8333	c.7881T>G	c.(7879-7881)gcT>gcG	p.A2627A	COL6A3_ENST00000353578.4_Silent_p.A2421A|COL6A3_ENST00000346358.4_Silent_p.A2427A|COL6A3_ENST00000347401.3_Silent_p.A2426A|COL6A3_ENST00000472056.1_Silent_p.A2020A|COL6A3_ENST00000409809.1_Silent_p.A2421A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2627	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A2627A(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGGTGGTCTCAGCGCTGTCTA	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											206.0	195.0	199.0					2																	238249678		2203	4300	6503	SO:0001819	synonymous_variant	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7881T>G	2.37:g.238249678A>C			A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2		NM_004369	
DDI1	414301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	103908554	103908554	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr11:103908554T>C	ENST00000302259.3	+	1	1247	c.1004T>C	c.(1003-1005)cTc>cCc	p.L335P	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)	335							aspartic-type endopeptidase activity (GO:0004190)	p.L335P(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)		CTAGATATGCTCCGGAGACAT	0.443																																																	2	Substitution - Missense(2)	kidney(2)											134.0	126.0	129.0					11																	103908554		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.1004T>C	11.37:g.103908554T>C	ENSP00000302805:p.Leu335Pro		Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.946953	0.53186	.	.	ENSG00000170967	ENST00000302259	T	0.68331	-0.32	5.21	5.21	0.72293	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.000000	0.64402	D	0.000001	D	0.85410	0.5690	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.88921	0.3366	10	0.87932	D	0	-7.9657	13.3819	0.60773	0.0:0.0:0.0:1.0	.	335	Q8WTU0	DDI1_HUMAN	P	335	ENSP00000302805:L335P	ENSP00000302805:L335P	L	+	2	0	DDI1	103413764	1.000000	0.71417	1.000000	0.80357	0.179000	0.23085	7.333000	0.79214	2.326000	0.78906	0.533000	0.62120	CTC		0.443	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1		NM_001001711	
GPR98	84059	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	90025457	90025457	+	Splice_Site	SNP	A	A	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr5:90025457A>C	ENST00000405460.2	+	50	10522		c.e50-1			NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98						detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.?(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCATTATTGCAGGAGATCAGA	0.289																																																	1	Unknown(1)	kidney(1)											110.0	94.0	99.0					5																	90025457		1799	4066	5865	SO:0001630	splice_region_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.10427-1A>C	5.37:g.90025457A>C			O75171|Q8TF58|Q9H0X5|Q9UL61	Splice_Site	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294008	0.60086	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000509621	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8658	0.70416	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR98	90061213	1.000000	0.71417	0.975000	0.42487	0.634000	0.38068	6.518000	0.73764	2.253000	0.74438	0.455000	0.32223	.		0.289	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2		NM_032119	Intron
H2AFJ	55766	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	14927791	14927791	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr12:14927791A>T	ENST00000544848.1	+	1	522	c.387A>T	c.(385-387)aaA>aaT	p.K129N		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	129						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K129N(1)		NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						CGAAGAGCAAATGACCCTGAC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											41.0	42.0	41.0					12																	14927791		2203	4300	6503	SO:0001583	missense	55766			AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"""Histones / Replication-independent"""	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.387A>T	12.37:g.14927791A>T	ENSP00000438553:p.Lys129Asn		Q9NV63	Missense_Mutation	SNP	ENST00000544848.1	37	CCDS31752.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.836562	0.32421	.	.	ENSG00000246705	ENST00000544848	D	0.83075	-1.68	4.64	2.83	0.33086	.	.	.	.	.	T	0.66426	0.2788	N	0.08118	0	0.35101	D	0.765267	B	0.10296	0.003	B	0.08055	0.003	T	0.67035	-0.5772	9	0.72032	D	0.01	.	9.3503	0.38133	0.177:0.0:0.823:0.0	.	129	Q9BTM1	H2AJ_HUMAN	N	129	ENSP00000438553:K129N	ENSP00000373730:K129N	K	+	3	2	H2AFJ	14819058	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.170000	0.31883	0.893000	0.36288	-0.137000	0.14449	AAA		0.607	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1		NM_177925	
HAGH	3029	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	1866933	1866933	+	Silent	SNP	G	G	A	rs201539587		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr16:1866933G>A	ENST00000397356.3	-	7	1114	c.708C>T	c.(706-708)ccC>ccT	p.P236P	HAGH_ENST00000455446.2_Missense_Mutation_p.P200L|HAGH_ENST00000397353.2_Silent_p.P188P|HAGH_ENST00000566709.1_Silent_p.P188P	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	236					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)	p.P188P(1)		kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CGGCATTGCCGGGCTCCACGT	0.627													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17457	0.0		0.0	False		,,,				2504	0.0				Pancreas(55;1048 1176 25227 40124 41333)												1	Substitution - coding silent(1)	kidney(1)											94.0	79.0	85.0					16																	1866933		2199	4300	6499	SO:0001819	synonymous_variant	3029			X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.708C>T	16.37:g.1866933G>A			A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	6.910	0.537450	0.13188	.	.	ENSG00000063854	ENST00000455446	.	.	.	4.97	-2.56	0.06268	.	0.000000	0.85682	D	0.000000	T	0.21186	0.0510	.	.	.	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.20739	-1.0266	8	0.06494	T	0.89	.	4.5759	0.12234	0.3059:0.0:0.3769:0.3172	.	200	E7EN93	.	L	200	.	ENSP00000406552:P200L	P	-	2	0	HAGH	1806934	0.002000	0.14202	0.109000	0.21407	0.436000	0.31835	-0.097000	0.11042	-0.070000	0.12908	-0.137000	0.14449	CCG		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2		NM_005326	
KCNJ10	3766	broad.mit.edu	37	1	160011200	160011200	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr1:160011200G>A	ENST00000368089.3	-	2	1349	c.1123C>T	c.(1123-1125)Cgc>Tgc	p.R375C	KCNJ10_ENST00000509700.1_Intron	NM_002241.4	NP_002232.2	P78508	KCJ10_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 10	375					adult walking behavior (GO:0007628)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|membrane hyperpolarization (GO:0060081)|optic nerve development (GO:0021554)|potassium ion homeostasis (GO:0055075)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of resting membrane potential (GO:0060075)|regulation of sensory perception of pain (GO:0051930)|response to blue light (GO:0009637)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)	p.R375S(1)|p.R375C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		Yohimbine(DB01392)	TTGCTGATGCGCACACTAAGG	0.532																																					GBM(167;1368 2014 14817 36425 43215)												2	Substitution - Missense(2)	lung(1)|kidney(1)											96.0	72.0	80.0					1																	160011200		2203	4300	6503	SO:0001583	missense	3766			U52155	CCDS1193.1	1q23.2	2011-07-05			ENSG00000177807	ENSG00000177807		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6256	protein-coding gene	gene with protein product		602208				9367690, 8995301, 16382105	Standard	NM_002241		Approved	Kir4.1, Kir1.2	uc001fuw.2	P78508	OTTHUMG00000024073	ENST00000368089.3:c.1123C>T	1.37:g.160011200G>A	ENSP00000357068:p.Arg375Cys		A3KME7|Q5VUT9|Q8N4I7|Q92808	Missense_Mutation	SNP	ENST00000368089.3	37	CCDS1193.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935814	0.52972	.	.	ENSG00000177807	ENST00000368089	D	0.90069	-2.61	4.77	4.77	0.60923	.	0.000000	0.44902	D	0.000419	D	0.84973	0.5591	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	P	0.60236	0.871	D	0.87512	0.2440	10	0.87932	D	0	.	10.4021	0.44235	0.0:0.0:0.8053:0.1947	.	375	P78508	IRK10_HUMAN	C	375	ENSP00000357068:R375C	ENSP00000357068:R375C	R	-	1	0	KCNJ10	158277824	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.070000	0.50033	2.489000	0.83994	0.655000	0.94253	CGC		0.532	KCNJ10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060629.1		NM_002241	
KIF13A	63971	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	17828563	17828563	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr6:17828563G>C	ENST00000259711.6	-	14	1545	c.1440C>G	c.(1438-1440)atC>atG	p.I480M	KIF13A_ENST00000378826.2_Missense_Mutation_p.I480M|KIF13A_ENST00000378816.5_Missense_Mutation_p.I480M|KIF13A_ENST00000378814.5_Missense_Mutation_p.I480M|KIF13A_ENST00000378843.2_Missense_Mutation_p.I480M	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	480	FHA.				ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I480M(2)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CAAAAAGCTGGATATCTTGAG	0.398																																																	2	Substitution - Missense(2)	kidney(2)											70.0	65.0	66.0					6																	17828563		1896	4116	6012	SO:0001583	missense	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1440C>G	6.37:g.17828563G>C	ENSP00000259711:p.Ile480Met		A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492925	0.64074	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	6.04	4.01	0.46588	Forkhead-associated (FHA) domain (3);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	D	0.93953	0.8064	H	0.95437	3.67	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.987;0.962;0.998;0.997	D	0.93602	0.6931	10	0.87932	D	0	.	4.9812	0.14166	0.1861:0.0:0.4529:0.361	.	451;480;480;480;480	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	M	480	ENSP00000368091:I480M;ENSP00000259711:I480M;ENSP00000368103:I480M;ENSP00000368120:I480M;ENSP00000368093:I480M	ENSP00000259711:I480M	I	-	3	3	KIF13A	17936542	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.666000	0.37460	1.491000	0.48482	0.563000	0.77884	ATC		0.398	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			
Unknown	0	broad.mit.edu	37	3	101431291	101431291	+	IGR	SNP	C	C	T			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr3:101431291C>T								RPL24 (25665 upstream) : CEP97 (11477 downstream)																							GCACAGCTGGCTTGAGCAACT	0.453																																																	0																																										SO:0001628	intergenic_variant	0																															3.37:g.101431291C>T				RNA	SNP		37																																																																																				0	0.453									
MACF1	23499	hgsc.bcm.edu;ucsc.edu	37	1	39781186	39781194	+	Splice_Site	DEL	ACACCCAGG	ACACCCAGG	-			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	ACACCCAGG	ACACCCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr1:39781186_39781194delACACCCAGG	ENST00000372915.3	+	26	3374_3382	c.3287_3295delACACCCAGG	c.(3286-3297)cacacccaggag>cag	p.1096_1099HTQE>Q	MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Splice_Site_p.1096_1099HTQE>Q|MACF1_ENST00000564288.1_Splice_Site_p.1091_1094HTQE>Q|MACF1_ENST00000545844.1_Splice_Site_p.1096_1099HTQE>Q|MACF1_ENST00000361689.2_Splice_Site_p.1096_1099HTQE>Q|MACF1_ENST00000317713.7_Splice_Site_p.1096_1099HTQE>Q|MACF1_ENST00000567887.1_Splice_Site_p.1128_1131HTQE>Q			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1096					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	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)			TCCTGGCAGCACACCCAGGAGGATTTACA	0.421																																																	0																																										SO:0001630	splice_region_variant	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.3286-1ACACCCAGG>-	1.37:g.39781186_39781194delACACCCAGG			B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	In_Frame_Del	DEL	ENST00000372915.3	37																																																																																					0.421	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1		NM_033044	In_Frame_Del
Unknown	0	broad.mit.edu	37	1	16974745	16974745	+	IGR	SNP	G	G	A	rs28526603	byFrequency	TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr1:16974745G>A								CROCCP2 (13691 upstream) : RNU1-3 (18534 downstream)																							CCTGGAACCGGAGGGCCGGGG	0.711																																																	0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16974745G>A				RNA	SNP		37																																																																																				0	0.711									
NOX3	50508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	155776182	155776182	+	Nonsense_Mutation	SNP	G	G	A	rs143358981		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr6:155776182G>A	ENST00000159060.2	-	2	232	c.130C>T	c.(130-132)Cga>Tga	p.R44*		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	44					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.R44*(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AAAATAACTCGTGTGTAATGG	0.343													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18049	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Nonsense(1)	kidney(1)						G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	68.0	65.0	66.0		130	4.7	1.0	6	dbSNP_134	66	5,8595	4.3+/-15.6	0,5,4295	yes	stop-gained	NOX3	NM_015718.2		0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461		44/569	155776182	6,13000	2203	4300	6503	SO:0001587	stop_gained	50508			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.130C>T	6.37:g.155776182G>A	ENSP00000159060:p.Arg44*		Q9HBJ9	Nonsense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	37	6.485134	0.97603	2.27E-4	5.81E-4	ENSG00000074771	ENST00000159060	.	.	.	5.61	4.73	0.59995	.	0.000000	0.52532	D	0.000073	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7291	11.4543	0.50171	0.0:0.13:0.7186:0.1514	.	.	.	.	X	44	.	ENSP00000159060:R44X	R	-	1	2	NOX3	155817874	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.049000	0.49869	1.460000	0.47911	-0.284000	0.09977	CGA		0.343	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			
ODF2	4957	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	131256884	131256884	+	Silent	SNP	A	A	G			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr9:131256884A>G	ENST00000434106.3	+	17	2211	c.1848A>G	c.(1846-1848)caA>caG	p.Q616Q	ODF2_ENST00000604420.1_Silent_p.Q616Q|ODF2_ENST00000351030.3_Silent_p.Q611Q|ODF2_ENST00000546203.1_Silent_p.Q597Q|ODF2_ENST00000372814.3_Silent_p.Q660Q|ODF2_ENST00000448249.3_Silent_p.Q535Q|ODF2_ENST00000444119.2_Silent_p.Q592Q|ODF2_ENST00000393527.3_Silent_p.Q592Q|ODF2_ENST00000372807.5_Silent_p.Q611Q|ODF2_ENST00000372791.3_Silent_p.Q597Q|ODF2_ENST00000393533.2_Silent_p.Q616Q	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	616					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.Q616Q(1)|p.Q592Q(1)|p.Q660Q(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GCCAAGACCAACTGCAGGGCT	0.587																																																	3	Substitution - coding silent(3)	kidney(3)											77.0	67.0	71.0					9																	131256884		2203	4300	6503	SO:0001819	synonymous_variant	4957			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1848A>G	9.37:g.131256884A>G			B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																				0.587	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			
P2RX3	5024	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	57118271	57118271	+	Silent	SNP	C	C	T			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr11:57118271C>T	ENST00000263314.2	+	8	775	c.741C>T	c.(739-741)tgC>tgT	p.C247C		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	247					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)	p.C247C(2)		endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						GCTGGGTGTGCGACTTGGACA	0.597																																																	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)											89.0	74.0	79.0					11																	57118271		2201	4296	6497	SO:0001819	synonymous_variant	5024			Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.741C>T	11.37:g.57118271C>T			Q6DK37|Q9UQB6	Silent	SNP	ENST00000263314.2	37	CCDS7953.1																																																																																				0.597	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1		NM_002559	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52621433	52621434	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr3:52621433_52621434delCT	ENST00000296302.7	-	19	3059_3060	c.3058_3059delAG	c.(3058-3060)agtfs	p.S1020fs	PBRM1_ENST00000337303.4_Frame_Shift_Del_p.S1020fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.S995fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.S1035fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.S995fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.S988fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.S1035fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.S1020fs			Q86U86	PB1_HUMAN	polybromo 1	1020	BAH 1. {ECO:0000255|PROSITE- ProRule:PRU00370}.				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)			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)		GTAATAGTCACTCTTAAAAACT	0.351			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0																																										SO:0001589	frameshift_variant	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.3058_3059delAG	3.37:g.52621435_52621436delCT	ENSP00000296302:p.Ser1020fs		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.351	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCSK6	5046	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	101933619	101933619	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr15:101933619delC	ENST00000348070.1	-	9	1003	c.1004delG	c.(1003-1005)ggcfs	p.G335fs	PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000358417.3_Frame_Shift_Del_p.G335fs|PCSK6_ENST00000398181.2_Frame_Shift_Del_p.G335fs|PCSK6_ENST00000344273.2_Frame_Shift_Del_p.G335fs|PCSK6_ENST00000331826.7_Frame_Shift_Del_p.G170fs	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	336	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGAGCCCAGGCCCTGCCGGCC	0.612																																																	0													39.0	46.0	43.0					15																	101933619		2183	4297	6480	SO:0001589	frameshift_variant	5046				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"""subtilisin-like protease"", ""subtilisin-like proprotein convertase 4"", ""subtilisin/kexin-like protease PACE4"""	167405	"""paired basic amino acid cleaving system 4"""	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.1004delG	15.37:g.101933619delC	ENSP00000305056:p.Gly335fs		Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Frame_Shift_Del	DEL	ENST00000348070.1	37																																																																																					0.612	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_002570	
PLEKHG4	25894	broad.mit.edu;hgsc.bcm.edu	37	16	67318759	67318759	+	Silent	SNP	G	G	A			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr16:67318759G>A	ENST00000360461.5	+	12	4371	c.1836G>A	c.(1834-1836)ctG>ctA	p.L612L	PLEKHG4_ENST00000450733.1_Silent_p.L531L|PLEKHG4_ENST00000379344.3_Silent_p.L612L|PLEKHG4_ENST00000427155.2_Silent_p.L612L	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	612							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L612L(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		TGTGGGCTCTGGCCACGGGGC	0.672																																																	1	Substitution - coding silent(1)	kidney(1)											18.0	20.0	19.0					16																	67318759		2196	4298	6494	SO:0001819	synonymous_variant	25894			AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1836G>A	16.37:g.67318759G>A			Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	37	CCDS32466.1																																																																																				0.672	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2		NM_015432	
SKIV2L	6499	broad.mit.edu;hgsc.bcm.edu	37	6	31932019	31932019	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr6:31932019T>C	ENST00000375394.2	+	17	1984	c.1871T>C	c.(1870-1872)aTg>aCg	p.M624T	SKIV2L_ENST00000544581.1_Missense_Mutation_p.M431T	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	624	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.M624T(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						GTCCTGCACATGTCAGAGCTC	0.597																																																	1	Substitution - Missense(1)	kidney(1)											106.0	77.0	87.0					6																	31932019		1510	2709	4219	SO:0001583	missense	6499				CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1871T>C	6.37:g.31932019T>C	ENSP00000364543:p.Met624Thr		O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	37	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	T	19.98	3.926401	0.73327	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.39997	1.05;1.05	5.95	5.95	0.96441	Helicase, C-terminal (2);	0.035850	0.85682	D	0.000000	T	0.54271	0.1848	M	0.76838	2.35	0.80722	D	1	D	0.60575	0.988	P	0.59056	0.851	T	0.61826	-0.6983	10	0.87932	D	0	-34.127	15.3985	0.74816	0.0:0.0:0.0:1.0	.	624	Q15477	SKIV2_HUMAN	T	624;466;431	ENSP00000364543:M624T;ENSP00000442645:M431T	ENSP00000364543:M624T	M	+	2	0	SKIV2L	32039998	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.988000	0.76212	2.279000	0.76181	0.533000	0.62120	ATG		0.597	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			
TEKT4	150483	hgsc.bcm.edu	37	2	95539855	95539855	+	Splice_Site	SNP	T	T	G	rs201662522	byFrequency	TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr2:95539855T>G	ENST00000295201.4	+	3	850		c.e3+2		AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4						cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CCAAGAGAGGTGGGCCCCAGC	0.682																																																	0													56.0	54.0	55.0					2																	95539855		2203	4300	6503	SO:0001630	splice_region_variant	150483			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.713+2T>G	2.37:g.95539855T>G				Splice_Site	SNP	ENST00000295201.4	37	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	13.70	2.316724	0.40996	.	.	ENSG00000163060	ENST00000295201	.	.	.	2.24	2.24	0.28232	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0143	0.30372	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TEKT4	94903582	1.000000	0.71417	0.603000	0.28903	0.057000	0.15508	4.740000	0.62087	0.779000	0.33543	0.254000	0.18369	.		0.682	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1		NM_144705	Intron
SMG1P7	100506060	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	T	C			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr16:70268080T>C	ENST00000459379.1	-	0	0																											GTCTTACTGTTGGCTAAAAGG	0.373																																																	0																																												0																															16.37:g.70268080T>C				RNA	SNP	ENST00000459379.1	37																																																																																					0.373	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
VHL	7428	broad.mit.edu	37	3	10183752	10183752	+	Missense_Mutation	SNP	T	T	A	rs5030803		TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr3:10183752T>A	ENST00000256474.2	+	1	1061	c.221T>A	c.(220-222)gTc>gAc	p.V74D	VHL_ENST00000345392.2_Missense_Mutation_p.V74D|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	74			V -> G (in VHLD; type I-II; dbSNP:rs5030803). {ECO:0000269|PubMed:8956040}.		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.V74D(8)|p.V74A(1)|p.S72_V87>L(1)|p.P71fs*84(1)|p.R60fs*35(1)|p.N67_V74del(1)|p.P71fs*56(1)|p.V74>?(1)|p.V74fs*77(1)|p.V74fs*82(1)|p.V74fs*51(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)		CCCTCCCAGGTCATCTTCTGC	0.721		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"""	18	Substitution - Missense(9)|Deletion - Frameshift(6)|Complex - deletion inframe(1)|Deletion - In frame(1)|Complex(1)	kidney(17)|soft_tissue(1)	GRCh37	CM961417	VHL	M	rs5030803						10.0	14.0	12.0					3																	10183752		2163	4233	6396	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.221T>A	3.37:g.10183752T>A	ENSP00000256474:p.Val74Asp		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.947597	0.92593	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.99842	-7.1;-7.1	5.34	4.16	0.48862	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.120953	0.56097	D	0.000027	D	0.99697	0.9885	M	0.73962	2.25	0.53688	D	0.999978	D;D	0.76494	0.998;0.999	D;D	0.70935	0.944;0.971	D	0.97903	1.0304	10	0.87932	D	0	-6.556	10.613	0.45434	0.0:0.0:0.1618:0.8382	.	74;74	P40337-2;P40337	.;VHL_HUMAN	D	74	ENSP00000256474:V74D;ENSP00000344757:V74D	ENSP00000256474:V74D	V	+	2	0	VHL	10158752	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.431000	0.52814	0.851000	0.35264	0.450000	0.29827	GTC		0.721	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VWA5A	4013	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	123995002	123995002	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr11:123995002G>A	ENST00000456829.2	+	11	1474	c.1223G>A	c.(1222-1224)aGg>aAg	p.R408K	VWA5A_ENST00000392744.4_Missense_Mutation_p.R424K|VWA5A_ENST00000361352.5_Missense_Mutation_p.R408K|VWA5A_ENST00000360334.4_Intron|VWA5A_ENST00000392748.1_Missense_Mutation_p.R408K|VWA5A_ENST00000449321.1_Missense_Mutation_p.R408K	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	408	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.							p.R408K(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						AAAGAAGTTAGGATCAACAGA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											91.0	86.0	88.0					11																	123995002		2201	4299	6500	SO:0001583	missense	4013			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1223G>A	11.37:g.123995002G>A	ENSP00000407726:p.Arg408Lys		Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	G	2.693	-0.272686	0.05716	.	.	ENSG00000110002	ENST00000456829;ENST00000392748;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02	5.68	-3.26	0.05064	von Willebrand factor, type A (3);	0.812122	0.11782	N	0.530109	T	0.03915	0.0110	N	0.16903	0.455	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.14023	0.002;0.01	T	0.46911	-0.9157	10	0.13108	T	0.6	-0.8526	6.902	0.24288	0.4104:0.0:0.4655:0.1241	.	424;408	B4DHS6;O00534	.;VMA5A_HUMAN	K	408;408;408;408;424	ENSP00000407726:R408K;ENSP00000376504:R408K;ENSP00000355070:R408K;ENSP00000404683:R408K;ENSP00000376501:R424K	ENSP00000355070:R408K	R	+	2	0	VWA5A	123500212	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.848000	0.04326	-0.601000	0.05783	-0.806000	0.03193	AGG		0.388	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1		NM_014622	
ZFYVE28	57732	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	2306052	2306052	+	Missense_Mutation	SNP	G	G	A	rs117669252	byFrequency	TCGA-BP-4975-01A-01D-1462-08	TCGA-BP-4975-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	109d2752-17f8-4b00-a61f-dfd8e2e3ca81	412ed2d9-14aa-4f99-8fb3-91713e0e43c9	g.chr4:2306052G>A	ENST00000290974.2	-	8	2354	c.2015C>T	c.(2014-2016)tCg>tTg	p.S672L	ZFYVE28_ENST00000511071.1_Missense_Mutation_p.S642L|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.S602L|RP11-478C1.7_ENST00000510632.1_RNA	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	672			S -> P (in dbSNP:rs661301). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.S672L(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						CTCGTGAGCCGAGGGGCTCCC	0.667													G|||	14	0.00279553	0.0068	0.0	5008	,	,		15583	0.005		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						G	LEU/SER,LEU/SER,LEU/SER	24,4374		0,24,2175	38.0	44.0	42.0		1925,1805,2015	1.4	0.0	4	dbSNP_132	42	2,8592		0,2,4295	yes	missense,missense,missense	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	145,145,145	0,26,6470	AA,AG,GG		0.0233,0.5457,0.2001	benign,benign,benign	642/858,602/818,672/888	2306052	26,12966	2199	4297	6496	SO:0001583	missense	57732			AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.2015C>T	4.37:g.2306052G>A	ENSP00000290974:p.Ser672Leu		B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	37	CCDS33942.1	9	0.004120879120879121	4	0.008130081300813009	0	0.0	5	0.008741258741258742	0	0.0	G	10.50	1.366827	0.24771	0.005457	2.33E-4	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.58506	0.33;0.33;0.33	3.14	1.36	0.22044	.	3.264500	0.00799	N	0.001410	T	0.25531	0.0621	N	0.03608	-0.345	0.09310	N	1	B;B	0.13145	0.007;0.0	B;B	0.04013	0.001;0.0	T	0.16748	-1.0392	10	0.29301	T	0.29	.	3.7751	0.08657	0.1314:0.0:0.629:0.2396	.	642;672	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	L	672;642;602	ENSP00000290974:S672L;ENSP00000425706:S642L;ENSP00000426299:S602L	ENSP00000290974:S672L	S	-	2	0	ZFYVE28	2275850	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	0.378000	0.20569	0.359000	0.24239	0.306000	0.20318	TCG		0.667	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1		XM_035371	
