#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
RBFOX1	54715	hgsc.bcm.edu;ucsc.edu	37	16	7726799	7726799	+	Nonsense_Mutation	SNP	C	C	G	rs182244522	byFrequency	TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr16:7726799C>G	ENST00000550418.1	+	14	1942	c.954C>G	c.(952-954)taC>taG	p.Y318*	RBFOX1_ENST00000553186.1_Nonsense_Mutation_p.Y291*|RBFOX1_ENST00000552089.1_Nonsense_Mutation_p.Y335*|RBFOX1_ENST00000340209.4_Nonsense_Mutation_p.Y323*|RBFOX1_ENST00000547338.1_Nonsense_Mutation_p.Y318*|RBFOX1_ENST00000422070.4_Nonsense_Mutation_p.Y361*|RBFOX1_ENST00000535565.2_Nonsense_Mutation_p.Y275*|RBFOX1_ENST00000547372.1_Nonsense_Mutation_p.Y361*|RBFOX1_ENST00000311745.5_Nonsense_Mutation_p.Y339*|RBFOX1_ENST00000355637.4_Nonsense_Mutation_p.Y339*|RBFOX1_ENST00000436368.2_Nonsense_Mutation_p.Y339*	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	318					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CATACCGCTACGCCCAGCCTA	0.517																																					Ovarian(157;934 2567 15163 39509)												0													193.0	133.0	153.0					16																	7726799		2197	4300	6497	SO:0001587	stop_gained	0			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.954C>G	16.37:g.7726799C>G	ENSP00000450031:p.Tyr318*	Somatic		WXS	SOLID	Phase_I	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Nonsense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	46	12.680426	0.99687	.	.	ENSG00000078328	ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	.	.	.	5.43	0.61	0.17580	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1439	6.958	0.24582	0.0:0.4022:0.0:0.5978	.	.	.	.	X	318;291;361;361;275;335;318;339;339;339;312;323	.	ENSP00000309117:Y339X	Y	+	3	2	RBFOX1	7666800	0.996000	0.38824	1.000000	0.80357	0.992000	0.81027	0.223000	0.17719	0.335000	0.23614	0.650000	0.86243	TAC		0.517	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2		NM_145891	
AFG3L2	10939	hgsc.bcm.edu;ucsc.edu	37	18	12337401	12337401	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr18:12337401A>G	ENST00000269143.3	-	16	2345	c.2114T>C	c.(2113-2115)aTt>aCt	p.I705T		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	705					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	AGCATCATTAATAAGTATTCG	0.413																																																	0													127.0	121.0	123.0					18																	12337401		2203	4300	6503	SO:0001583	missense	10939			Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"""ATPases / AAA-type"""	315	protein-coding gene	gene with protein product		604581	"""AFG3 (ATPase family gene 3, yeast)-like 2"", ""spinocerebellar ataxia 28"", ""AFG3 ATPase family gene 3-like 2 (yeast)"", ""AFG3 ATPase family gene 3-like 2 (S. cerevisiae)"", ""AFG3 ATPase family member 3-like 2 (S. cerevisiae)"""	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2114T>C	18.37:g.12337401A>G	ENSP00000269143:p.Ile705Thr	Somatic		WXS	SOLID	Phase_I	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	37	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.347579	0.82022	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	D	0.84660	-1.88	5.62	5.62	0.85841	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.090429	0.64402	D	0.000001	D	0.93006	0.7774	M	0.86953	2.85	0.80722	D	1	D	0.64830	0.994	D	0.71184	0.972	D	0.93981	0.7258	10	0.66056	D	0.02	-8.4566	15.8226	0.78667	1.0:0.0:0.0:0.0	.	705	Q9Y4W6	AFG32_HUMAN	T	705;720	ENSP00000269143:I705T	ENSP00000269143:I705T	I	-	2	0	AFG3L2	12327401	1.000000	0.71417	0.997000	0.53966	0.946000	0.59487	8.871000	0.92346	2.146000	0.66826	0.533000	0.62120	ATT		0.413	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2		NM_006796	
ATP11C	286410	hgsc.bcm.edu;ucsc.edu	37	X	138840003	138840003	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chrX:138840003C>G	ENST00000327569.3	-	23	2771	c.2673G>C	c.(2671-2673)caG>caC	p.Q891H	ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000361648.2_Missense_Mutation_p.Q891H|ATP11C_ENST00000359686.2_Missense_Mutation_p.Q891H|ATP11C_ENST00000370557.1_Missense_Mutation_p.Q885H|ATP11C_ENST00000370543.1_Missense_Mutation_p.Q891H	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	891					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					GGTACAAAAACTGTGGCAAAA	0.284																																																	0													28.0	26.0	27.0					X																	138840003		2203	4291	6494	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.2673G>C	X.37:g.138840003C>G	ENSP00000332756:p.Gln891His	Somatic		WXS	SOLID	Phase_I	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377919	0.61735	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43	5.66	-2.48	0.06423	.	0.000000	0.85682	D	0.000000	D	0.91486	0.7312	M	0.65677	2.01	0.45662	D	0.998587	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.88000	0.2755	10	0.27082	T	0.32	.	13.2742	0.60178	0.0:0.427:0.0:0.573	.	891;891;891	Q8NB49-3;Q8NB49;Q8NB49-2	.;AT11C_HUMAN;.	H	885;891;891;891;891	ENSP00000359588:Q885H;ENSP00000355165:Q891H;ENSP00000332756:Q891H;ENSP00000359574:Q891H;ENSP00000352715:Q891H	ENSP00000332756:Q891H	Q	-	3	2	ATP11C	138667669	0.052000	0.20516	0.984000	0.44739	0.985000	0.73830	-0.602000	0.05680	-0.461000	0.06993	-0.268000	0.10319	CAG		0.284	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1		NM_173694	
VWA7	80737	hgsc.bcm.edu;ucsc.edu	37	6	31743892	31743892	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr6:31743892C>G	ENST00000375688.4	-	3	562	c.362G>C	c.(361-363)aGg>aCg	p.R121T	VWA7_ENST00000467576.1_Intron|Y_RNA_ENST00000364685.1_RNA|VWA7_ENST00000447450.1_Missense_Mutation_p.R121T|VWA7_ENST00000375686.3_Missense_Mutation_p.R121T			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	121						extracellular region (GO:0005576)											GGGGTCATTCCTGGAAGTTGG	0.632																																																	0													106.0	99.0	101.0					6																	31743892		2203	4300	6503	SO:0001583	missense	0				CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"""chromosome 6 open reading frame 27"""	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.362G>C	6.37:g.31743892C>G	ENSP00000364840:p.Arg121Thr	Somatic		WXS	SOLID	Phase_I	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627151	0.28978	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.12984	2.63;2.63;2.63	5.32	-8.73	0.00841	.	0.481167	0.21028	N	0.081392	T	0.04497	0.0123	L	0.39898	1.24	0.09310	N	1	B	0.34290	0.447	B	0.35114	0.196	T	0.01639	-1.1306	10	0.45353	T	0.12	-3.2507	19.9896	0.97361	0.0:0.783:0.0:0.217	.	121	Q9Y334	G7C_HUMAN	T	121	ENSP00000364840:R121T;ENSP00000364838:R121T;ENSP00000390554:R121T	ENSP00000364838:R121T	R	-	2	0	C6orf27	31851871	0.000000	0.05858	0.006000	0.13384	0.020000	0.10135	-1.474000	0.02337	-1.327000	0.02264	-0.438000	0.05819	AGG		0.632	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2		NM_025258	
COL4A6	1288	hgsc.bcm.edu;ucsc.edu	37	X	107420105	107420105	+	Silent	SNP	C	C	T			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chrX:107420105C>T	ENST00000372216.4	-	28	2755	c.2655G>A	c.(2653-2655)ggG>ggA	p.G885G	COL4A6_ENST00000394872.2_Silent_p.G885G|COL4A6_ENST00000545689.1_Silent_p.G884G|COL4A6_ENST00000334504.7_Silent_p.G884G|COL4A6_ENST00000538570.1_Silent_p.G884G	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	885	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						ACCCAGCGACCCCTGGAGAGC	0.547									Alport syndrome with Diffuse Leiomyomatosis																												Melanoma(87;1895 1945 2589 7165)												0													121.0	123.0	123.0					X																	107420105		2203	4300	6503	SO:0001819	synonymous_variant	1288	Familial Cancer Database		U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.2655G>A	X.37:g.107420105C>T		Somatic		WXS	SOLID	Phase_I	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	37	CCDS14541.1																																																																																				0.547	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			
COX18	285521	hgsc.bcm.edu;ucsc.edu	37	4	73927583	73927583	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr4:73927583A>T	ENST00000295890.4	-	5	866	c.775T>A	c.(775-777)Ttt>Att	p.F259I	COX18_ENST00000507544.2_Missense_Mutation_p.F260I	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	259					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCACGGACAAAGTACGTAATA	0.393																																																	0													110.0	92.0	98.0					4																	73927583		2203	4300	6503	SO:0001583	missense	285521			AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"""Mitochondrial respiratory chain complex assembly factors"""	26801	protein-coding gene	gene with protein product		610428	"""COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)"", ""cytochrome c oxidase assembly homolog 18 (yeast)"""			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.775T>A	4.37:g.73927583A>T	ENSP00000295890:p.Phe259Ile	Somatic		WXS	SOLID	Phase_I	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Missense_Mutation	SNP	ENST00000295890.4	37	CCDS3554.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868828	0.32977	.	.	ENSG00000163626	ENST00000295890;ENST00000507544	.	.	.	5.22	5.22	0.72569	.	0.141076	0.64402	D	0.000004	T	0.56775	0.2008	L	0.52364	1.645	0.47994	D	0.999562	B;B	0.16166	0.016;0.003	B;B	0.28709	0.093;0.026	T	0.52056	-0.8626	9	0.13108	T	0.6	-20.0584	14.3915	0.66983	1.0:0.0:0.0:0.0	.	260;259	B7ZL88;Q8N8Q8	.;COX18_HUMAN	I	259;260	.	ENSP00000295890:F259I	F	-	1	0	COX18	74146447	1.000000	0.71417	0.949000	0.38748	0.027000	0.11550	3.972000	0.56838	2.103000	0.63969	0.455000	0.32223	TTT		0.393	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2		NM_173827	
IL6R	3570	hgsc.bcm.edu;ucsc.edu	37	1	154401718	154401718	+	Silent	SNP	T	T	A			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr1:154401718T>A	ENST00000368485.3	+	2	569	c.132T>A	c.(130-132)acT>acA	p.T44T	IL6R_ENST00000344086.4_Silent_p.T44T	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	44	Ig-like C2-type.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	ACAGCGTGACTCTGACCTGCC	0.637																																																	0													79.0	77.0	78.0					1																	154401718		2203	4300	6503	SO:0001819	synonymous_variant	3570			X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.132T>A	1.37:g.154401718T>A		Somatic		WXS	SOLID	Phase_I	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Silent	SNP	ENST00000368485.3	37	CCDS1067.1																																																																																				0.637	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1		NM_000565	
TLDC1	57707	hgsc.bcm.edu	37	16	84523001	84523001	+	Missense_Mutation	SNP	C	C	T	rs531177116		TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr16:84523001C>T	ENST00000343629.6	-	4	594	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	TLDC1_ENST00000561807.1_5'UTR|TLDC1_ENST00000535580.1_Missense_Mutation_p.V111M	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	138						lysosomal membrane (GO:0005765)		p.V138L(1)									AGCACGTGCACCACAGAGCCA	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	ovary(1)											56.0	52.0	53.0					16																	84523001		2200	4300	6500	SO:0001583	missense	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.412G>A	16.37:g.84523001C>T	ENSP00000343635:p.Val138Met	Somatic		WXS	SOLID	Phase_I	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249594	0.59212	.	.	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.15834	2.39;2.39	5.04	4.06	0.47325	.	0.399254	0.27522	N	0.018990	T	0.33323	0.0859	M	0.74258	2.255	0.09310	N	0.999997	D;P	0.69078	0.997;0.722	D;B	0.63192	0.912;0.231	T	0.11941	-1.0567	10	0.41790	T	0.15	-5.9212	6.4774	0.22043	0.0:0.6849:0.1552:0.1599	.	111;138	F5GWS3;Q6P9B6	.;K1609_HUMAN	M	138;111	ENSP00000343635:V138M;ENSP00000441997:V111M	ENSP00000343635:V138M	V	-	1	0	KIAA1609	83080502	0.008000	0.16893	0.101000	0.21167	0.991000	0.79684	1.505000	0.35736	1.069000	0.40788	0.591000	0.81541	GTG		0.542	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1		NM_020947	
MAP1B	4131	hgsc.bcm.edu;ucsc.edu	37	5	71493194	71493194	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr5:71493194C>T	ENST00000296755.7	+	5	4310	c.4012C>T	c.(4012-4014)Caa>Taa	p.Q1338*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1338					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ACCTTACTATCAATCTCCTAC	0.458																																					Melanoma(17;367 822 11631 31730 47712)												0													68.0	66.0	67.0					5																	71493194		2203	4300	6503	SO:0001587	stop_gained	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4012C>T	5.37:g.71493194C>T	ENSP00000296755:p.Gln1338*	Somatic		WXS	SOLID	Phase_I	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	45	11.330628	0.99547	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.3218	19.877	0.96880	0.0:1.0:0.0:0.0	.	.	.	.	X	1338	.	ENSP00000296755:Q1338X	Q	+	1	0	MAP1B	71528950	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.487000	0.81328	2.709000	0.92574	0.561000	0.74099	CAA		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6		NM_005909	
PHKG1	5260	hgsc.bcm.edu	37	7	56155438	56155438	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr7:56155438G>A	ENST00000297373.2	-	3	309	c.115C>T	c.(115-117)Cac>Tac	p.H39Y	PHKG1_ENST00000537360.1_Missense_Mutation_p.P3L|PHKG1_ENST00000452681.2_Missense_Mutation_p.H39Y|PHKG1_ENST00000489604.1_5'UTR	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	39	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GTGGGCTTGTGGATGCATCGC	0.662																																					Melanoma(184;580 2064 5329 24177 35303)												0													62.0	50.0	54.0					7																	56155438		2203	4300	6503	SO:0001583	missense	5260			X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.115C>T	7.37:g.56155438G>A	ENSP00000297373:p.His39Tyr	Somatic		WXS	SOLID	Phase_I	B7Z1D0|F5H2S1|Q75LP5	Missense_Mutation	SNP	ENST00000297373.2	37	CCDS5525.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.40|15.40	2.822613|2.822613	0.50739|0.50739	.|.	.|.	ENSG00000164776|ENSG00000164776	ENST00000452681;ENST00000297373|ENST00000537360	T;T|T	0.66995|0.68624	-0.24;-0.24|-0.34	5.42|5.42	4.52|4.52	0.55395|0.55395	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.251525|.	0.35067|.	N|.	0.003461|.	T|T	0.63534|0.63534	0.2519|0.2519	M|M	0.69248|0.69248	2.105|2.105	0.31085|0.31085	N|N	0.711465|0.711465	B;B;B|B	0.21381|0.02656	0.055;0.016;0.027|0.0	B;B;B|B	0.25140|0.04013	0.058;0.012;0.057|0.001	T|T	0.65274|0.65274	-0.6208|-0.6208	10|9	0.87932|0.87932	D|D	0|0	-54.168|-54.168	9.4005|9.4005	0.38428|0.38428	0.158:0.0:0.842:0.0|0.158:0.0:0.842:0.0	.|.	39;39;39|3	B7Z6U2;F5H2S1;Q16816|B7Z5U3	.;.;PHKG1_HUMAN|.	Y|L	39|3	ENSP00000445440:H39Y;ENSP00000297373:H39Y|ENSP00000441528:P3L	ENSP00000297373:H39Y|ENSP00000441528:P3L	H|P	-|-	1|2	0|0	PHKG1|PHKG1	56122932|56122932	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.746000|2.746000	0.47467|0.47467	2.712000|2.712000	0.92718|0.92718	0.563000|0.563000	0.77884|0.77884	CAC|CCA		0.662	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1		NM_006213	
PTCH1	5727	hgsc.bcm.edu	37	9	98240434	98240434	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr9:98240434T>G	ENST00000331920.6	-	9	1549	c.1250A>C	c.(1249-1251)cAa>cCa	p.Q417P	PTCH1_ENST00000429896.2_Missense_Mutation_p.Q266P|PTCH1_ENST00000375274.2_Missense_Mutation_p.Q416P|PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000421141.1_Missense_Mutation_p.Q266P|PTCH1_ENST00000437951.1_Missense_Mutation_p.Q351P|PTCH1_ENST00000418258.1_Missense_Mutation_p.Q266P|PTCH1_ENST00000430669.2_Missense_Mutation_p.Q351P	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	417					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.Q417fs*29(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AAGCACCTTTTGAGTGGAGTT	0.517																																																	1	Insertion - Frameshift(1)	skin(1)											232.0	183.0	200.0					9																	98240434		2203	4300	6503	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1250A>C	9.37:g.98240434T>G	ENSP00000332353:p.Gln417Pro	Somatic		WXS	SOLID	Phase_I	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825068	0.90955	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.75;-2.7	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92987	0.7768	L	0.47190	1.495	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.997;0.997	D;P;D;D	0.69479	0.96;0.888;0.964;0.953	D	0.92249	0.5807	10	0.36615	T	0.2	-20.1995	15.8498	0.78921	0.0:0.0:0.0:1.0	.	266;351;416;417	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	P	417;351;266;266;351;266;416;134	ENSP00000332353:Q417P;ENSP00000389744:Q351P;ENSP00000399981:Q266P;ENSP00000396135:Q266P;ENSP00000410287:Q351P;ENSP00000414823:Q266P;ENSP00000364423:Q416P;ENSP00000364420:Q134P	ENSP00000332353:Q417P	Q	-	2	0	PTCH1	97280255	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.157000	0.67596	0.533000	0.62120	CAA		0.517	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2		NM_000264	
RYR1	6261	hgsc.bcm.edu;ucsc.edu	37	19	39002238	39002238	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr19:39002238G>A	ENST00000359596.3	+	61	9160	c.9160G>A	c.(9160-9162)Gtc>Atc	p.V3054I	RYR1_ENST00000355481.4_Missense_Mutation_p.V3054I|RYR1_ENST00000360985.3_Missense_Mutation_p.V3054I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3054					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCGCCACCGAGTCTCTCTCTT	0.522																																																	0													164.0	147.0	152.0					19																	39002238		2203	4300	6503	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9160G>A	19.37:g.39002238G>A	ENSP00000352608:p.Val3054Ile	Somatic		WXS	SOLID	Phase_I	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.050388	0.36181	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.66460	-0.21;-0.21;-0.21	4.55	4.55	0.56014	.	0.000000	0.64402	U	0.000014	T	0.34774	0.0909	N	0.02011	-0.69	0.37575	D	0.919573	B;B	0.24258	0.1;0.06	B;B	0.17098	0.017;0.008	T	0.42050	-0.9474	10	0.07482	T	0.82	.	12.3662	0.55230	0.0841:0.0:0.9158:0.0	.	3054;3054	P21817-2;P21817	.;RYR1_HUMAN	I	3054	ENSP00000352608:V3054I;ENSP00000347667:V3054I;ENSP00000354254:V3054I	ENSP00000347667:V3054I	V	+	1	0	RYR1	43694078	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	1.764000	0.38471	2.536000	0.85505	0.491000	0.48974	GTC		0.522	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			
SLC27A6	28965	hgsc.bcm.edu;ucsc.edu	37	5	128368807	128368807	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr5:128368807G>A	ENST00000262462.4	+	10	2702	c.1692G>A	c.(1690-1692)atG>atA	p.M564I	SLC27A6_ENST00000395266.1_Missense_Mutation_p.M564I|SLC27A6_ENST00000506176.1_Missense_Mutation_p.M564I			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	564					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		AGGAAAAAATGGAAGCAACAG	0.289																																																	0													48.0	47.0	47.0					5																	128368807		2203	4294	6497	SO:0001583	missense	28965			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.1692G>A	5.37:g.128368807G>A	ENSP00000262462:p.Met564Ile	Somatic		WXS	SOLID	Phase_I	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	5.344	0.248711	0.10130	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.54279	0.58;0.58;0.58	3.85	3.85	0.44370	.	0.155066	0.56097	D	0.000028	T	0.33352	0.0860	N	0.11106	0.095	0.40102	D	0.976383	B	0.17038	0.02	B	0.17722	0.019	T	0.13361	-1.0512	9	.	.	.	-5.0952	16.6631	0.85246	0.0:0.0:1.0:0.0	.	564	Q9Y2P4	S27A6_HUMAN	I	564	ENSP00000262462:M564I;ENSP00000378684:M564I;ENSP00000421024:M564I	.	M	+	3	0	SLC27A6	128396706	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.659000	0.68010	2.451000	0.82905	0.585000	0.79938	ATG		0.289	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1		NM_014031	
STAT1	6772	hgsc.bcm.edu;ucsc.edu	37	2	191849113	191849113	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4777-01A-01D-1366-10	TCGA-BP-4777-11A-01D-1367-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd4d15-8a3a-49f1-b6f9-236ae5262be3	74aadb21-b60b-438f-8eb6-6f163f77d21d	g.chr2:191849113G>C	ENST00000361099.3	-	16	1657	c.1270C>G	c.(1270-1272)Ctc>Gtc	p.L424V	STAT1_ENST00000409465.1_Missense_Mutation_p.L424V|STAT1_ENST00000392323.2_Missense_Mutation_p.L426V|STAT1_ENST00000392322.3_Missense_Mutation_p.L424V|STAT1_ENST00000540176.1_3'UTR	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	424					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			GTAACGATGAGAGGACCCTTG	0.408																																																	0													60.0	65.0	63.0					2																	191849113		2203	4300	6503	SO:0001583	missense	6772				CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.1270C>G	2.37:g.191849113G>C	ENSP00000354394:p.Leu424Val	Somatic		WXS	SOLID	Phase_I	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507665	0.64410	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	5.15	4.27	0.50696	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.063289	0.64402	D	0.000004	T	0.81432	0.4821	M	0.67625	2.065	0.80722	D	1	P;B	0.44734	0.842;0.088	P;B	0.49665	0.618;0.193	T	0.83156	-0.0101	10	0.62326	D	0.03	-4.9585	13.7209	0.62725	0.0746:0.0:0.9254:0.0	.	424;424	P42224-2;P42224	.;STAT1_HUMAN	V	424;424;424;426	ENSP00000354394:L424V;ENSP00000386244:L424V;ENSP00000376136:L424V;ENSP00000376137:L426V	ENSP00000354394:L424V	L	-	1	0	STAT1	191557358	1.000000	0.71417	0.962000	0.40283	0.784000	0.44337	6.401000	0.73256	1.310000	0.45006	0.561000	0.74099	CTC		0.408	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3		NM_007315	
