#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	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_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
DUSP27	92235	hgsc.bcm.edu	37	1	167097085	167097085	+	Missense_Mutation	SNP	A	A	C	rs377480316		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:167097085A>C	ENST00000361200.2	+	6	2883	c.2717A>C	c.(2716-2718)aAa>aCa	p.K906T	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.K906T|DUSP27_ENST00000271385.5_Missense_Mutation_p.K906T			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	906	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AATTCCCAGAAACCTGAAACA	0.493																																					p.K906T		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2717C						PASS	.	A	THR/LYS	0,4406		0,0,2203	87.0	77.0	81.0		2717	1.5	1.0	1		81	1,8599	1.2+/-3.3	0,1,4299	no	missense	DUSP27	NM_001080426.1	78	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	probably-damaging	906/1159	167097085	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			CCCAGAAACCTGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2717A>C	chr1.hg19:g.167097085A>C	ENSP00000354483:p.Lys906Thr	66.0	0.0	.		56.0	5.0	.	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.356232	0.41700	0.0	1.16E-4	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.04454	3.62;3.62;3.62	5.25	1.46	0.22682	.	0.874767	0.09948	N	0.735044	T	0.01905	0.0060	M	0.65975	2.015	0.09310	N	1	P	0.35433	0.501	B	0.27608	0.081	T	0.42899	-0.9424	10	0.87932	D	0	-19.6906	5.4857	0.16749	0.6201:0.1386:0.2413:0.0	.	906	Q5VZP5	DUS27_HUMAN	T	906	ENSP00000354483:K906T;ENSP00000271385:K906T;ENSP00000404874:K906T	ENSP00000271385:K906T	K	+	2	0	DUSP27	165363709	0.258000	0.24033	0.973000	0.42090	0.754000	0.42855	1.679000	0.37597	0.315000	0.23110	-0.269000	0.10298	AAA	.	.	.	none		0.493	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217279802	217279802	+	Silent	SNP	C	C	G			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr2:217279802C>G	ENST00000357276.4	+	3	705	c.375C>G	c.(373-375)ccC>ccG	p.P125P	AC098820.2_ENST00000457694.1_RNA|SMARCAL1_ENST00000358207.5_Silent_p.P125P	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	125					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		TCTCTCCTCCCTTGGCACAAA	0.507									Schimke Immuno-Osseous Dysplasia																												p.P125P		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.C375G						PASS	.						88.0	80.0	82.0					2																	217279802		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon3	Familial Cancer Database	SIOD	TCCTCCCTTGGCA	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.375C>G	chr2.hg19:g.217279802C>G		105.0	0.0	.		109.0	44.0	.	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1																																																																																			.	.	.	none		0.507	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
APEH	327	hgsc.bcm.edu	37	3	49723522	49723522	+	IGR	SNP	G	G	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr3:49723522G>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.R374C|MST1_ENST00000494828.2_5'Flank	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.R360C(2)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCTGTACAACGCCGGATCTGG	0.697																																					p.R374C		Atlas-SNP	.											MST1,NS,carcinoma,0,2	MST1	84	.	2	Substitution - Missense(2)	lung(1)|central_nervous_system(1)	c.C1120T						PASS	.						12.0	14.0	13.0					3																	49723522		2191	4284	6475	SO:0001628	intergenic_variant	4485	exon9			TACAACGCCGGAT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49723522G>A		40.0	2.0	.		30.0	4.0	.	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037157	0.93630	.	.	ENSG00000173531	ENST00000449682	T	0.68181	-0.31	5.4	4.52	0.55395	.	0.000000	0.42682	D	0.000669	D	0.83078	0.5176	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.83214	-0.0072	10	0.32370	T	0.25	.	13.2202	0.59883	0.0778:0.0:0.9222:0.0	.	374	G3XAK1	.	C	374	ENSP00000414287:R374C	ENSP00000414287:R374C	R	-	1	0	MST1	49698526	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	8.008000	0.88588	2.526000	0.85167	0.655000	0.94253	CGT	.	.	.	none		0.697	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
PARK2	5071	hgsc.bcm.edu	37	6	162206852	162206852	+	Missense_Mutation	SNP	G	G	C	rs34424986	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr6:162206852G>C	ENST00000366898.1	-	7	925	c.823C>G	c.(823-825)Cgg>Ggg	p.R275G	PARK2_ENST00000338468.3_Missense_Mutation_p.R84G|PARK2_ENST00000366894.1_Missense_Mutation_p.R84G|PARK2_ENST00000366896.1_Missense_Mutation_p.R126G|PARK2_ENST00000366892.1_Missense_Mutation_p.R275G|PARK2_ENST00000366897.1_Missense_Mutation_p.R247G	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	275	SYT11 binding 2.		R -> W (in PARK2 and PARK; at heterozygosity it is associated with late onset Parkinson disease; impairs the ability to ubiquitinate SNCAIP; abolishes p53/TP53 transcriptional repression; dbSNP:rs34424986). {ECO:0000269|PubMed:10072423, ECO:0000269|PubMed:10824074, ECO:0000269|PubMed:11179010, ECO:0000269|PubMed:11971093, ECO:0000269|PubMed:12114481, ECO:0000269|PubMed:12116199, ECO:0000269|PubMed:12730996, ECO:0000269|PubMed:22956510}.		adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		ACAAACTGCCGATCATTGAGT	0.478																																					p.R275G		Atlas-SNP	.											PARK2_ENST00000366892,NS,malignant_melanoma,0,2	PARK2	96	.	0			c.C823G	GRCh37	CM991007	PARK2	M	rs34424986	PASS	.						102.0	88.0	93.0					6																	162206852		2203	4300	6503	SO:0001583	missense	5071	exon7			ACTGCCGATCATT		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"""Parkinson disease"""	8607	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase"""	602544	"""Parkinson disease (autosomal recessive, juvenile) 2, parkin"", ""parkinson protein 2, E3 ubiquitin protein ligase (parkin)"""			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.823C>G	chr6.hg19:g.162206852G>C	ENSP00000355865:p.Arg275Gly	48.0	0.0	.		42.0	2.0	.	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	hg19	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643036	0.67244	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.6;-2.6;-2.6	5.75	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.92322	0.7564	M	0.83483	2.645	0.36075	D	0.842404	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;0.961	D;D;D;D;P	0.91635	0.999;0.987;0.999;0.999;0.666	D	0.91610	0.5302	10	0.25106	T	0.35	.	14.0915	0.64993	0.0:0.0:0.849:0.151	.	275;126;247;275;84	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	G	275;247;126;84;84;84;275;196	ENSP00000355865:R275G;ENSP00000355863:R247G;ENSP00000355862:R126G;ENSP00000355860:R84G;ENSP00000343589:R84G;ENSP00000355858:R275G	ENSP00000343589:R84G	R	-	1	2	PARK2	162126842	0.982000	0.34865	0.751000	0.31187	0.863000	0.49368	1.685000	0.37659	1.406000	0.46857	0.650000	0.86243	CGG	.	G|0.998;A|0.002	.	alt		0.478	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1		
TBP	6908	hgsc.bcm.edu	37	6	170871091	170871091	+	Silent	SNP	G	G	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr6:170871091G>A	ENST00000392092.2	+	3	546	c.267G>A	c.(265-267)caG>caA	p.Q89Q	TBP_ENST00000230354.6_Silent_p.Q89Q|TBP_ENST00000540980.1_Silent_p.Q69Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	89	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.617																																					p.Q89Q		Atlas-SNP	.											TBP,NS,carcinoma,0,1	TBP	58	.	0			c.G267A						PASS	.						20.0	26.0	24.0					6																	170871091		1890	3708	5598	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAGCAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.267G>A	chr6.hg19:g.170871091G>A		60.0	0.0	.		71.0	3.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.617	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
FBXW2	26190	hgsc.bcm.edu	37	9	123527053	123527053	+	Silent	SNP	G	G	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr9:123527053G>A	ENST00000608872.1	-	8	1336	c.1149C>T	c.(1147-1149)gaC>gaT	p.D383D	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Silent_p.D318D	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	383					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						GGTAGCGGTTGTCAAACAGCA	0.502																																					p.D383D		Atlas-SNP	.											.	FBXW2	34	.	0			c.C1149T						PASS	.						92.0	90.0	91.0					9																	123527053		1949	4160	6109	SO:0001819	synonymous_variant	26190	exon8			GCGGTTGTCAAAC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13608	protein-coding gene	gene with protein product		609071	"""F-box and WD-40 domain protein 2"""			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1149C>T	chr9.hg19:g.123527053G>A		139.0	0.0	.		125.0	11.0	.	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Silent	SNP	ENST00000608872.1	hg19	CCDS43872.1																																																																																			.	.	.	none		0.502	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2		
MMP13	4322	hgsc.bcm.edu	37	11	102826393	102826393	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:102826393C>A	ENST00000260302.3	-	1	70	c.42G>T	c.(40-42)tgG>tgT	p.W14C	MMP13_ENST00000340273.4_Missense_Mutation_p.W14C	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	14					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	GACAATGAGTCCAGCTCAAGA	0.507																																					p.W14C		Atlas-SNP	.											.	MMP13	75	.	0			c.G42T						PASS	.						94.0	94.0	94.0					11																	102826393		2202	4299	6501	SO:0001583	missense	4322	exon1			ATGAGTCCAGCTC	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.42G>T	chr11.hg19:g.102826393C>A	ENSP00000260302:p.Trp14Cys	114.0	0.0	.		101.0	10.0	.	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	6.549	0.469578	0.12461	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.15139	2.64;2.45	5.87	5.87	0.94306	.	0.442712	0.26311	N	0.025120	T	0.11024	0.0269	N	0.14661	0.345	0.47994	D	0.999562	P	0.48640	0.913	B	0.40741	0.339	T	0.03306	-1.1050	10	0.45353	T	0.12	.	11.7621	0.51910	0.1372:0.7305:0.1323:0.0	.	14	P45452	MMP13_HUMAN	C	14	ENSP00000260302:W14C;ENSP00000339672:W14C	ENSP00000260302:W14C	W	-	3	0	MMP13	102331603	0.998000	0.40836	0.987000	0.45799	0.168000	0.22595	1.956000	0.40382	2.941000	0.99782	0.655000	0.94253	TGG	.	.	.	none		0.507	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						PASS	.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	29.0	0.0	.		37.0	19.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
MTUS2	23281	hgsc.bcm.edu	37	13	29599704	29599704	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr13:29599704C>T	ENST00000431530.3	+	1	957	c.899C>T	c.(898-900)tCg>tTg	p.S300L		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	290						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.S300L(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						ACTTTGGCATCGAAGGAAATC	0.507																																					p.S300L		Atlas-SNP	.											MTUS2_ENST00000431530,colon,carcinoma,-1,2	MTUS2	279	.	2	Substitution - Missense(2)	endometrium(1)|central_nervous_system(1)	c.C899T						PASS	.						40.0	40.0	40.0					13																	29599704		2007	4188	6195	SO:0001583	missense	23281	exon1			TGGCATCGAAGGA	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.899C>T	chr13.hg19:g.29599704C>T	ENSP00000392057:p.Ser300Leu	32.0	0.0	.		32.0	9.0	.	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.391325	0.25118	.	.	ENSG00000132938	ENST00000431530	T	0.13089	2.62	5.49	0.716	0.18191	.	0.981254	0.08305	N	0.966293	T	0.06096	0.0158	N	0.03115	-0.41	0.09310	N	1	B	0.21309	0.054	B	0.12156	0.007	T	0.44128	-0.9348	9	.	.	.	.	10.4835	0.44708	0.0:0.587:0.0:0.413	.	290	Q5JR59	MTUS2_HUMAN	L	300	ENSP00000392057:S300L	.	S	+	2	0	MTUS2	28497704	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.040000	0.13905	0.015000	0.14971	0.561000	0.74099	TCG	.	.	.	none		0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
SLC8A3	6547	hgsc.bcm.edu	37	14	70527578	70527578	+	Silent	SNP	C	C	T	rs376675749		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:70527578C>T	ENST00000381269.2	-	3	2616	c.1863G>A	c.(1861-1863)ccG>ccA	p.P621P	SLC8A3_ENST00000216568.7_5'UTR|SLC8A3_ENST00000533541.1_Intron|SLC8A3_ENST00000528359.1_Intron|SLC8A3_ENST00000357887.3_Intron|SLC8A3_ENST00000394330.2_Intron|SLC8A3_ENST00000534137.1_Silent_p.P621P|SLC8A3_ENST00000356921.2_Silent_p.P621P|SLC8A3_ENST00000533899.1_5'UTR	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	621					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CCATCCATTTCGGTTCACCAA	0.343																																					p.P621P		Atlas-SNP	.											SLC8A3,caecum,carcinoma,0,1	SLC8A3	234	.	0			c.G1863A						PASS	.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	167.0	144.0	152.0		,,1863,1863,,1863	5.9	1.0	14		152	0,8600		0,0,4300	no	utr-5,intron,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,,,,	,,621/925,621/922,,621/928	70527578	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon3			CCATTTCGGTTCA	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1863G>A	chr14.hg19:g.70527578C>T		101.0	0.0	.		71.0	22.0	.	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	hg19	CCDS35498.1																																																																																			.	.	.	weak		0.343	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
TRIP11	9321	hgsc.bcm.edu	37	14	92470654	92470654	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:92470654T>A	ENST00000267622.4	-	11	4039	c.3666A>T	c.(3664-3666)gaA>gaT	p.E1222D		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1222					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GCTTCCACTCTTCCATTTTCT	0.443			T	PDGFRB	AML																																p.E1222D	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.A3666T						PASS	.						79.0	72.0	75.0					14																	92470654		2203	4300	6503	SO:0001583	missense	9321	exon11			CCACTCTTCCATT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.3666A>T	chr14.hg19:g.92470654T>A	ENSP00000267622:p.Glu1222Asp	78.0	0.0	.		64.0	28.0	.	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.88|11.88	1.771464|1.771464	0.31320|0.31320	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.05786|.	3.39|.	5.46|5.46	-4.33|-4.33	0.03677|0.03677	.|.	0.112824|.	0.64402|.	D|.	0.000015|.	T|.	0.44664|.	0.1304|.	L|L	0.32530|0.32530	0.975|0.975	0.41458|0.41458	D|D	0.988026|0.988026	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.91635|.	0.78;0.999|.	T|.	0.32745|.	-0.9895|.	10|.	0.52906|.	T|.	0.07|.	.|.	8.2632|8.2632	0.31797|0.31797	0.119:0.4845:0.0:0.3964|0.119:0.4845:0.0:0.3964	.|.	958;1222|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	D|X	1222;958|938	ENSP00000267622:E1222D|.	ENSP00000267622:E1222D|.	E|R	-|-	3|1	2|2	TRIP11|TRIP11	91540407|91540407	0.238000|0.238000	0.23825|0.23825	0.822000|0.822000	0.32727|0.32727	0.150000|0.150000	0.21749|0.21749	-0.435000|-0.435000	0.06931|0.06931	-1.215000|-1.215000	0.02610|0.02610	-0.624000|-0.624000	0.04008|0.04008	GAA|AGA	.	.	.	none		0.443	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
ATP10A	57194	hgsc.bcm.edu	37	15	25972305	25972305	+	Splice_Site	SNP	A	A	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr15:25972305A>T	ENST00000356865.6	-	4	959		c.e4+1			NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCCCGAGCCTACCTGCGTAGA	0.517																																					.		Atlas-SNP	.											.	ATP10A	270	.	0			c.847+2T>A						PASS	.						102.0	81.0	88.0					15																	25972305		2203	4300	6503	SO:0001630	splice_region_variant	57194	exon5			GAGCCTACCTGCG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.847+1T>A	chr15.hg19:g.25972305A>T		86.0	0.0	.		81.0	36.0	.	NM_024490	Q4G0S9|Q969I4	Splice_Site	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514606	0.85389	.	.	ENSG00000206190	ENST00000356865	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3129	0.74048	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP10A	23523398	1.000000	0.71417	0.995000	0.50966	0.813000	0.45954	8.600000	0.90860	2.033000	0.60031	0.460000	0.39030	.	.	.	.	none		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	Intron
SRCAP	10847	hgsc.bcm.edu	37	16	30718524	30718524	+	Silent	SNP	G	G	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30718524G>T	ENST00000262518.4	+	5	712	c.327G>T	c.(325-327)cgG>cgT	p.R109R	SRCAP_ENST00000344771.4_Silent_p.R109R|SRCAP_ENST00000395059.2_Silent_p.R109R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	109					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCGAGACTCGGATTGCTGAGC	0.547																																					p.R109R		Atlas-SNP	.											.	SRCAP	298	.	0			c.G327T						PASS	.						69.0	69.0	69.0					16																	30718524		1987	4166	6153	SO:0001819	synonymous_variant	10847	exon5			GACTCGGATTGCT	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.327G>T	chr16.hg19:g.30718524G>T		77.0	0.0	.		90.0	34.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.547	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
SRCAP	10847	hgsc.bcm.edu	37	16	30727477	30727477	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30727477T>C	ENST00000262518.4	+	17	2969	c.2584T>C	c.(2584-2586)Tcc>Ccc	p.S862P	SRCAP_ENST00000344771.4_Missense_Mutation_p.S862P|SRCAP_ENST00000395059.2_Missense_Mutation_p.S862P	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	862					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CTGCAGGCTCTCCAAGCGTCA	0.517																																					p.S862P		Atlas-SNP	.											.	SRCAP	298	.	0			c.T2584C						PASS	.						137.0	119.0	125.0					16																	30727477		2197	4300	6497	SO:0001583	missense	10847	exon17			AGGCTCTCCAAGC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2584T>C	chr16.hg19:g.30727477T>C	ENSP00000262518:p.Ser862Pro	105.0	0.0	.		117.0	5.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735012	0.69189	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.79749	-1.3;-1.3;-1.3	5.25	5.25	0.73442	SNF2-related (1);	0.000000	0.53938	D	0.000054	D	0.89577	0.6755	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.90981	0.4827	10	0.87932	D	0	-15.3089	14.2776	0.66191	0.0:0.0:0.0:1.0	.	862;862;862	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	P	862	ENSP00000262518:S862P;ENSP00000378499:S862P;ENSP00000343042:S862P	ENSP00000262518:S862P	S	+	1	0	SRCAP	30634978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.712000	0.84684	2.201000	0.70794	0.459000	0.35465	TCC	.	.	.	none		0.517	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
LYZL6	57151	hgsc.bcm.edu	37	17	34261844	34261844	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:34261844C>T	ENST00000585556.1	-	5	737	c.403G>A	c.(403-405)Ggc>Agc	p.G135S	LYZL6_ENST00000492340.2_5'Flank|LYZL6_ENST00000293274.4_Missense_Mutation_p.G135S|LYZL6_ENST00000394523.3_Missense_Mutation_p.G135S			O75951	LYZL6_HUMAN	lysozyme-like 6	135					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGTGGCCGGCCTGAACAGTGC	0.542																																					p.G135S		Atlas-SNP	.											.	LYZL6	18	.	0			c.G403A						PASS	.						89.0	82.0	85.0					17																	34261844		2203	4300	6503	SO:0001583	missense	57151	exon4			GCCGGCCTGAACA	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.403G>A	chr17.hg19:g.34261844C>T	ENSP00000468094:p.Gly135Ser	83.0	0.0	.		77.0	19.0	.	NM_020426	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	hg19	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410784	0.62399	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.51325	0.71;0.71	4.65	4.65	0.58169	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000004	T	0.66336	0.2779	M	0.87547	2.89	0.23988	N	0.996253	D	0.57257	0.979	P	0.56088	0.791	T	0.63844	-0.6545	10	0.62326	D	0.03	-0.303	13.7598	0.62959	0.0:1.0:0.0:0.0	.	135	O75951	LYZL6_HUMAN	S	135	ENSP00000293274:G135S;ENSP00000378031:G135S	ENSP00000293274:G135S	G	-	1	0	LYZL6	31285957	0.058000	0.20735	0.004000	0.12327	0.101000	0.19017	2.826000	0.48104	2.518000	0.84900	0.563000	0.77884	GGC	.	.	.	none		0.542	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48600413	48600413	+	Silent	SNP	A	A	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:48600413A>T	ENST00000323776.5	+	11	1662	c.1500A>T	c.(1498-1500)cgA>cgT	p.R500R	MYCBPAP_ENST00000436259.2_Silent_p.R463R	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ATGACTGGCGACGGCAGCACC	0.507																																					p.R500R		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.A1500T						PASS	.						108.0	105.0	106.0					17																	48600413		2203	4300	6503	SO:0001819	synonymous_variant	84073	exon11			CTGGCGACGGCAG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1500A>T	chr17.hg19:g.48600413A>T		165.0	0.0	.		144.0	54.0	.	NM_032133		Silent	SNP	ENST00000323776.5	hg19	CCDS32680.2																																																																																			.	.	.	none		0.507	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
ZNF626	199777	hgsc.bcm.edu	37	19	20807580	20807581	+	Missense_Mutation	DNP	GG	GG	AA			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:20807580_20807581GG>AA	ENST00000601440.1	-	4	1248_1249	c.1102_1103CC>TT	c.(1102-1104)CCc>TTc	p.P368F	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						ACATTTGTAGGGTTTCTCTCCA	0.396																																					p.P368L|p.P368S		Atlas-SNP	.											.	ZNF626	121	.	0			c.C1103T|c.C1102T						PASS	.																																			SO:0001583	missense	199777	exon4			TTGTAGGGTTTCT|TGTAGGGTTTCTC	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1102_1103delinsAA	chr19.hg19:g.20807580_20807581delinsAA	ENSP00000469958:p.Pro368Phe	94.0|96.0	0.0	.		84.0	6.0	.	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.	.	none		0.396	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
ZNF431	170959	hgsc.bcm.edu	37	19	21365595	21365595	+	Silent	SNP	G	G	A			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:21365595G>A	ENST00000311048.7	+	5	633	c.489G>A	c.(487-489)gaG>gaA	p.E163E	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000600692.1_3'UTR	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	163					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						GTTATAATGAGCTAAACCAGT	0.328																																					p.E163E		Atlas-SNP	.											ZNF431,colon,carcinoma,0,2	ZNF431	71	.	0			c.G489A						PASS	.																																			SO:0001819	synonymous_variant	170959	exon5			TAATGAGCTAAAC	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"""Zinc fingers, C2H2-type"", ""-"""	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.489G>A	chr19.hg19:g.21365595G>A		68.0	2.0	.		98.0	16.0	.	NM_133473	A8KAK7|Q8IWC4	Silent	SNP	ENST00000311048.7	hg19	CCDS32979.1																																																																																			.	.	.	none		0.328	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098	
IFNL1	282618	hgsc.bcm.edu	37	19	39787490	39787490	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:39787490T>G	ENST00000333625.2	+	2	314	c.217T>G	c.(217-219)Ttc>Gtc	p.F73V		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	73					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										CTCTCCTGTCTTCCCCGGGAA	0.572																																					p.F73V		Atlas-SNP	.											.	.	.	.	0			c.T217G						PASS	.						91.0	86.0	88.0					19																	39787490		2203	4300	6503	SO:0001583	missense	282618	exon2			CCTGTCTTCCCCG	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"""Interferons"""	18363	protein-coding gene	gene with protein product		607403	"""interleukin 29"", ""interleukin 29 (interferon, lambda 1)"""	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.217T>G	chr19.hg19:g.39787490T>G	ENSP00000329991:p.Phe73Val	99.0	0.0	.		120.0	5.0	.	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	hg19	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470360	0.63625	.	.	ENSG00000182393	ENST00000333625	T	0.35421	1.31	3.69	3.69	0.42338	.	0.094954	0.46758	D	0.000269	T	0.59770	0.2218	M	0.84846	2.72	0.25011	N	0.991407	D	0.71674	0.998	D	0.71870	0.975	T	0.54098	-0.8344	10	0.66056	D	0.02	-28.5284	10.3642	0.44012	0.0:0.0:0.0:1.0	.	73	Q8IU54	IL29_HUMAN	V	73	ENSP00000329991:F73V	ENSP00000329991:F73V	F	+	1	0	IL29	44479330	0.956000	0.32656	0.939000	0.37840	0.068000	0.16541	1.113000	0.31184	1.553000	0.49476	0.374000	0.22700	TTC	.	.	.	none		0.572	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140	
CCM2L	140706	hgsc.bcm.edu	37	20	30617596	30617596	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr20:30617596G>T	ENST00000300415.8	+	9	1370	c.1357G>T	c.(1357-1359)Ggc>Tgc	p.G453C	CCM2L_ENST00000262659.8_Missense_Mutation_p.Q431H|RP1-310O13.7_ENST00000449519.1_RNA			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	453																	CTATTGCACAGGCCTGCTGAA	0.637																																					p.Q431H		Atlas-SNP	.											C20orf160_ENST00000300415,colon,carcinoma,0,2	.	.	.	0			c.G1293T						PASS	.						63.0	58.0	60.0					20																	30617596		2203	4300	6503	SO:0001583	missense	140706	exon8			TGCACAGGCCTGC	AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 160"""	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.1357G>T	chr20.hg19:g.30617596G>T	ENSP00000300415:p.Gly453Cys	105.0	0.0	.		122.0	6.0	.	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.66|15.66	2.898002|2.898002	0.52227|0.52227	.|.	.|.	ENSG00000101331|ENSG00000101331	ENST00000300415;ENST00000452892|ENST00000262659	T;T|T	0.37411|0.65916	1.2;1.2|-0.18	5.65|5.65	4.64|4.64	0.57946|0.57946	.|.	0.293408|.	0.36778|.	N|.	0.002419|.	T|T	0.58935|0.58935	0.2157|0.2157	.|.	.|.	.|.	0.28263|0.28263	N|N	0.924728|0.924728	D|B	0.63046|0.33512	0.992|0.415	P|B	0.56216|0.34301	0.794|0.179	T|T	0.60727|0.60727	-0.7206|-0.7206	9|8	0.62326|0.66056	D|D	0.03|0.02	-45.7996|-45.7996	17.3707|17.3707	0.87376|0.87376	0.0:0.1353:0.8647:0.0|0.0:0.1353:0.8647:0.0	.|.	453|431	Q9NUG4|Q9NUG4-2	CT160_HUMAN|.	C|H	453;206|431	ENSP00000300415:G453C;ENSP00000392448:G206C|ENSP00000262659:Q431H	ENSP00000300415:G453C|ENSP00000262659:Q431H	G|Q	+|+	1|3	0|2	C20orf160|C20orf160	30081257|30081257	1.000000|1.000000	0.71417|0.71417	0.960000|0.960000	0.40013|0.40013	0.898000|0.898000	0.52572|0.52572	3.363000|3.363000	0.52321|0.52321	2.648000|2.648000	0.89879|0.89879	0.563000|0.563000	0.77884|0.77884	GGC|CAG	.	.	.	none		0.637	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625	
PHKA2	5256	hgsc.bcm.edu	37	X	18972370	18972370	+	Splice_Site	SNP	A	A	G			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrX:18972370A>G	ENST00000379942.4	-	2	903		c.e2+1			NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)						carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					AGTCACTATTACCTGCTCCAG	0.537																																					.		Atlas-SNP	.											.	PHKA2	122	.	0			c.237+2T>C						PASS	.						138.0	107.0	117.0					X																	18972370		2203	4300	6503	SO:0001630	splice_region_variant	5256	exon3			ACTATTACCTGCT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.237+1T>C	chrX.hg19:g.18972370A>G		73.0	0.0	.		95.0	4.0	.	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Splice_Site	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266542	0.59540	.	.	ENSG00000044446	ENST00000379942	.	.	.	5.54	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0604	0.47944	0.8588:0.0:0.0:0.1412	.	.	.	.	.	-1	.	.	.	-	.	.	PHKA2	18882291	1.000000	0.71417	0.991000	0.47740	0.625000	0.37756	9.284000	0.95882	0.713000	0.32060	0.486000	0.48141	.	.	.	.	none		0.537	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	Intron
MT-ND1	4535	hgsc.bcm.edu	37	M	4117	4117	+	Silent	SNP	T	T	C			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrM:4117T>C	ENST00000361390.2	+	1	811	c.811T>C	c.(811-813)Tta>Cta	p.L271L	MT-TC_ENST00000387405.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-ND2_ENST00000361453.3_5'Flank|MT-RNR1_ENST00000389680.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	271					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCTCCCTGTTCTTATGAATTC	0.433																																					p.L271L		Atlas-SNP	.											.	.	.	.	0			c.T811C						PASS	.																																			SO:0001819	synonymous_variant	10625	exon1			CTGTTCTTATGAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.811T>C	chrM.hg19:g.4117T>C		0.0	0.0	.		7.0	6.0	.	ENST00000361390	C0JKH6|Q37523	Silent	SNP	ENST00000361390.2	hg19																																																																																				.	.	.	none		0.433	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8470	8470	+	Silent	SNP	A	A	G			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrM:8470A>G	ENST00000361851.1	+	1	105	c.105A>G	c.(103-105)ctA>ctG	p.L35L	MT-ND4L_ENST00000361335.1_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	35					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										AACTACCACCTACCTCCCTCA	0.398																																					p.L35L		Atlas-SNP	.											.	.	.	.	0			c.A105G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CCACCTACCTCCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.105A>G	chrM.hg19:g.8470A>G		0.0	0.0	.		11.0	11.0	.	ENST00000361851	Q34771	Silent	SNP	ENST00000361851.1	hg19																																																																																				.	.	.	none		0.398	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
BICD1	636	hgsc.bcm.edu	37	12	32491723	32491724	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:32491723_32491724delAT	ENST00000281474.5	+	8	2677_2678	c.2574_2575delAT	c.(2572-2577)caatttfs	p.QF858fs	BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	858					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			CTGCAAGACAATTTTCACCTTC	0.406																																					p.858_858del		Atlas-INDEL	.											.	BICD1	89	.	0			c.2573_2574del						PASS	.																																			SO:0001589	frameshift_variant	636	exon8			.	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2574_2575delAT	chr12.hg19:g.32491723_32491724delAT	ENSP00000281474:p.Gln858fs	200.0	0.0	0		182.0	62.0	0.340659	NM_001714	A8K2C3|F8W113|O43892|O43893	Frame_Shift_Del	DEL	ENST00000281474.5	hg19	CCDS8726.1																																																																																			.	.	.	none		0.406	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
