#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
A1CF	29974	hgsc.bcm.edu	37	10	52575931	52575931	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr10:52575931C>A	ENST00000373993.1	-	7	1020	c.976G>T	c.(976-978)Gag>Tag	p.E326*	A1CF_ENST00000374001.2_Nonsense_Mutation_p.E326*|A1CF_ENST00000395489.2_Nonsense_Mutation_p.E319*|A1CF_ENST00000373997.3_Nonsense_Mutation_p.E326*|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000282641.2_Nonsense_Mutation_p.E326*|A1CF_ENST00000395495.1_Nonsense_Mutation_p.E271*|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000373995.3_Nonsense_Mutation_p.E334*			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	326					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.E326K(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						TAGGTATACTCTCCTTGCAGC	0.517																																																	1	Substitution - Missense(1)	central_nervous_system(1)											187.0	178.0	181.0					10																	52575931		2203	4300	6503	SO:0001587	stop_gained	29974			AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.976G>T	10.37:g.52575931C>A	ENSP00000363105:p.Glu326*	Somatic		WXS	SOLID	Phase_I	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Nonsense_Mutation	SNP	ENST00000373993.1	37	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	C	37	5.981570	0.97168	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489	.	.	.	5.69	5.69	0.88448	.	0.258209	0.43579	D	0.000558	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	17.2909	0.87156	0.0:1.0:0.0:0.0	.	.	.	.	X	326;326;326;334;326;271;309;319	.	ENSP00000282641:E326X	E	-	1	0	A1CF	52245937	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	7.448000	0.80631	2.690000	0.91761	0.650000	0.86243	GAG		0.517	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2		NM_014576	
ACP1	52	hgsc.bcm.edu	37	2	265004	265004	+	Missense_Mutation	SNP	C	C	G	rs147428558		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr2:265004C>G	ENST00000272065.5	+	1	133	c.40C>G	c.(40-42)Ctg>Gtg	p.L14V	SH3YL1_ENST00000403712.2_5'Flank|SH3YL1_ENST00000405430.1_5'Flank|ACP1_ENST00000405233.1_Missense_Mutation_p.L14V|ACP1_ENST00000407983.3_Missense_Mutation_p.L14V|SH3YL1_ENST00000402632.1_5'Flank|ACP1_ENST00000272067.6_Missense_Mutation_p.L14V|SH3YL1_ENST00000356150.5_5'Flank|SH3YL1_ENST00000403658.1_5'Flank|ACP1_ENST00000439645.2_Missense_Mutation_p.L14V|SH3YL1_ENST00000468321.1_5'Flank	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	14				CLGNICRS -> PARREAAR (in Ref. 5; AAB27085). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	GTTTGTGTGTCTGGGTAAGAG	0.647																																																	0													176.0	138.0	151.0					2																	265004		2203	4300	6503	SO:0001583	missense	52			M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.40C>G	2.37:g.265004C>G	ENSP00000272065:p.Leu14Val	Somatic		WXS	SOLID	Phase_I	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.933859	0.52866	.	.	ENSG00000143727	ENST00000272067;ENST00000272065;ENST00000407983;ENST00000439645;ENST00000405233;ENST00000449425	T;T;T;T;T	0.30714	2.22;2.22;1.52;2.22;2.22	4.21	1.35	0.21983	Phosphotyrosine protein phosphatase I superfamily (3);	0.000000	0.64402	D	0.000003	T	0.39682	0.1087	M	0.73430	2.235	0.80722	D	1	B;B;B	0.29136	0.023;0.001;0.234	B;B;B	0.42692	0.041;0.012;0.395	T	0.31166	-0.9953	10	0.87932	D	0	-6.2011	6.8407	0.23961	0.0:0.6044:0.0:0.3956	.	14;14;14	P24666-2;P24666;B5MCC7	.;PPAC_HUMAN;.	V	14	ENSP00000272067:L14V;ENSP00000272065:L14V;ENSP00000385404:L14V;ENSP00000408596:L14V;ENSP00000384307:L14V	ENSP00000272065:L14V	L	+	1	2	ACP1	255004	1.000000	0.71417	0.997000	0.53966	0.597000	0.36814	0.931000	0.28871	0.152000	0.19188	0.591000	0.81541	CTG		0.647	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3			
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18906804	18906804	+	Silent	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:18906804G>A	ENST00000380548.4	+	28	5415	c.5076G>A	c.(5074-5076)gtG>gtA	p.V1692V	ADAMTSL1_ENST00000380545.5_Silent_p.V393V	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1692	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CCCGGCGTGTGGAGTGTGTGC	0.632																																																	0													54.0	69.0	64.0					9																	18906804		2135	4225	6360	SO:0001819	synonymous_variant	92949			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.5076G>A	9.37:g.18906804G>A		Somatic		WXS	SOLID	Phase_I	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																				0.632	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			
AP3S1	1176	hgsc.bcm.edu	37	5	115202418	115202421	+	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs80118146		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr5:115202418_115202421delAAGA	ENST00000316788.7	+	2	678_681	c.121_124delAAGA	c.(121-126)aagagafs	p.KR41fs		NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	41					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		TTTGGTATCTAAGAGAGATGAAAA	0.304																																																	0																																										SO:0001589	frameshift_variant	1176			D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.121_124delAAGA	5.37:g.115202418_115202421delAAGA	ENSP00000325369:p.Lys41fs	Somatic		WXS	SOLID	Phase_I	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Frame_Shift_Del	DEL	ENST00000316788.7	37	CCDS4123.1																																																																																				0.304	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2			
ARFGEF1	10565	hgsc.bcm.edu;ucsc.edu	37	8	68111228	68111228	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr8:68111228C>T	ENST00000262215.3	-	39	5880	c.5491G>A	c.(5491-5493)Gga>Aga	p.G1831R	ARFGEF1_ENST00000517955.1_5'UTR|ARFGEF1_ENST00000520381.1_Intron	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1831					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.G1831R(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			AAAACTACTCCGATTCGCAGA	0.373																																																	1	Substitution - Missense(1)	large_intestine(1)											145.0	136.0	139.0					8																	68111228		2203	4300	6503	SO:0001583	missense	10565			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.5491G>A	8.37:g.68111228C>T	ENSP00000262215:p.Gly1831Arg	Somatic		WXS	SOLID	Phase_I	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.436273	0.83885	.	.	ENSG00000066777	ENST00000262215	T	0.34275	1.37	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.61874	0.2382	M	0.82823	2.61	0.80722	D	1	D;D	0.71674	0.997;0.998	P;P	0.59546	0.859;0.852	T	0.67654	-0.5615	10	0.87932	D	0	.	19.0957	0.93249	0.0:1.0:0.0:0.0	.	1831;655	Q9Y6D6;B3KMS9	BIG1_HUMAN;.	R	1831	ENSP00000262215:G1831R	ENSP00000262215:G1831R	G	-	1	0	ARFGEF1	68273782	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	7.776000	0.85560	2.672000	0.90937	0.650000	0.86243	GGA		0.373	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4		NM_006421	
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chrX:2833631A>G	ENST00000381154.1	-	6	1041	c.966T>C	c.(964-966)taT>taC	p.Y322Y	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	322					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CATTATCACCATATAAGCCAT	0.507																																																	0													236.0	159.0	185.0					X																	2833631		2203	4300	6503	SO:0001819	synonymous_variant	414			X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.966T>C	X.37:g.2833631A>G		Somatic		WXS	SOLID	Phase_I	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																				0.507	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1			
PTCD1	26024	hgsc.bcm.edu;ucsc.edu	37	7	99017741	99017741	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr7:99017741A>G	ENST00000292478.4	-	8	2202	c.1952T>C	c.(1951-1953)aTt>aCt	p.I651T	PTCD1_ENST00000555673.1_Missense_Mutation_p.I700T|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.I700T	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	651					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GAAGCCGTCAATCTTCTCCAG	0.547																																																	0													108.0	115.0	113.0					7																	99017741		2203	4300	6503	SO:0001583	missense	100526740			AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1952T>C	7.37:g.99017741A>G	ENSP00000292478:p.Ile651Thr	Somatic		WXS	SOLID	Phase_I	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227565	0.79576	.	.	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.69435	-0.4;-0.36;-0.36	5.82	4.68	0.58851	.	0.101095	0.64402	D	0.000003	T	0.78065	0.4225	M	0.70595	2.14	0.49213	D	0.999768	D;D	0.76494	0.999;0.997	D;P	0.67382	0.951;0.88	T	0.80103	-0.1522	10	0.66056	D	0.02	-17.7665	11.2922	0.49256	0.9293:0.0:0.0707:0.0	.	700;651	G3V325;O75127	.;PTCD1_HUMAN	T	651;433;700;700	ENSP00000292478:I651T;ENSP00000450995:I700T;ENSP00000400168:I700T	ENSP00000400168:I700T	I	-	2	0	ATP5J2-PTCD1;PTCD1	98855677	1.000000	0.71417	0.978000	0.43139	0.887000	0.51463	7.171000	0.77595	2.215000	0.71742	0.459000	0.35465	ATT		0.547	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1		NM_015545	
ATP8B4	79895	hgsc.bcm.edu;ucsc.edu	37	15	50215637	50215637	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr15:50215637A>T	ENST00000284509.6	-	17	1838	c.1697T>A	c.(1696-1698)cTg>cAg	p.L566Q	ATP8B4_ENST00000559829.1_Missense_Mutation_p.L566Q	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	566						Golgi apparatus (GO:0005794)|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)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TTTTTCAAACAGAATAGTATC	0.388																																																	0													78.0	72.0	74.0					15																	50215637		2196	4295	6491	SO:0001583	missense	79895			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1697T>A	15.37:g.50215637A>T	ENSP00000284509:p.Leu566Gln	Somatic		WXS	SOLID	Phase_I	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463533	0.84425	.	.	ENSG00000104043	ENST00000284509	D	0.85258	-1.96	4.93	4.93	0.64822	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.272230	0.30076	N	0.010464	D	0.91429	0.7295	M	0.78456	2.415	0.45777	D	0.998669	D	0.61080	0.989	D	0.71184	0.972	D	0.92378	0.5911	10	0.87932	D	0	.	12.8303	0.57742	1.0:0.0:0.0:0.0	.	566	Q8TF62	AT8B4_HUMAN	Q	566	ENSP00000284509:L566Q	ENSP00000284509:L566Q	L	-	2	0	ATP8B4	48002929	0.976000	0.34144	1.000000	0.80357	0.995000	0.86356	9.037000	0.93765	1.979000	0.57680	0.533000	0.62120	CTG		0.388	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1		NM_024837	
BICD1	636	hgsc.bcm.edu	37	12	32481360	32481360	+	Silent	SNP	G	G	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr12:32481360G>C	ENST00000281474.5	+	5	2074	c.1971G>C	c.(1969-1971)cgG>cgC	p.R657R	BICD1_ENST00000548411.1_Silent_p.R657R	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	657					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)			CAGCGGCTCGGGAGCTAGCCC	0.502																																																	0													68.0	72.0	71.0					12																	32481360		2203	4300	6503	SO:0001819	synonymous_variant	636			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.1971G>C	12.37:g.32481360G>C		Somatic		WXS	SOLID	Phase_I	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																				0.502	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1		NM_001714	
ELP5	23587	hgsc.bcm.edu	37	17	7160242	7160242	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr17:7160242G>A	ENST00000396628.2	+	5	741	c.524G>A	c.(523-525)gGc>gAc	p.G175D	ELP5_ENST00000574993.1_Missense_Mutation_p.G175D|ELP5_ENST00000396627.2_Missense_Mutation_p.G175D|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000354429.2_Missense_Mutation_p.G175D|ELP5_ENST00000356683.2_Missense_Mutation_p.G175D	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	175				G -> S (in Ref. 1; AAM10496). {ECO:0000305}.	chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											CATGGACCAGGCCCTGTGGGA	0.597																																																	0													72.0	61.0	65.0					17																	7160242		2203	4300	6503	SO:0001583	missense	0			BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.524G>A	17.37:g.7160242G>A	ENSP00000379869:p.Gly175Asp	Somatic		WXS	SOLID	Phase_I	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	37	CCDS11094.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712319	0.48517	.	.	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.54479	1.37;1.37;1.37;0.57	5.32	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.68238	0.2979	M	0.68952	2.095	0.50632	D	0.999886	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.74348	0.972;0.983;0.971	T	0.70923	-0.4740	10	0.62326	D	0.03	-23.0859	12.1862	0.54241	0.0:0.172:0.828:0.0	.	175;175;175	Q8TE02-2;A8K1M5;Q8TE02	.;.;DERP6_HUMAN	D	175	ENSP00000346412:G175D;ENSP00000379869:G175D;ENSP00000379868:G175D;ENSP00000349111:G175D	ENSP00000346412:G175D	G	+	2	0	C17orf81	7100966	0.990000	0.36364	0.999000	0.59377	0.342000	0.28953	2.840000	0.48215	1.353000	0.45828	0.655000	0.94253	GGC		0.597	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1		NM_015362	
BRCA1	672	hgsc.bcm.edu	37	17	41267787	41267787	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr17:41267787C>A	ENST00000357654.3	-	3	208	c.90G>T	c.(88-90)ttG>ttT	p.L30F	BRCA1_ENST00000352993.3_Missense_Mutation_p.L30F|BRCA1_ENST00000351666.3_Missense_Mutation_p.L30F|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000309486.4_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.L30F|BRCA1_ENST00000468300.1_Missense_Mutation_p.L30F|BRCA1_ENST00000491747.2_Missense_Mutation_p.L30F|BRCA1_ENST00000493795.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.L30F|BRCA1_ENST00000354071.3_Missense_Mutation_p.L30F	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	30			L -> F (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L30F(2)		NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTTCCTTGATCAACTCCAGAC	0.343			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																													yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	2	Substitution - Missense(2)	breast(2)											54.0	49.0	50.0					17																	41267787		2203	4300	6503	SO:0001583	missense	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.90G>T	17.37:g.41267787C>A	ENSP00000350283:p.Leu30Phe	Somatic		WXS	SOLID	Phase_I	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600248	0.66332	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000468300;ENST00000471181;ENST00000491747;ENST00000478531;ENST00000470026;ENST00000477152;ENST00000494123;ENST00000476777;ENST00000489037	D;D;D;D;D;D;D;D;D;D;D;D;D;D;T	0.95001	-2.18;-3.58;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;3.22	5.97	1.84	0.25277	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.40469	N	0.001081	D	0.94928	0.8360	L	0.48362	1.52	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.85130	0.997;0.997;0.995;0.995;0.997;0.997;0.99	D	0.93003	0.6425	10	0.87932	D	0	-5.6223	8.4708	0.32984	0.0:0.7072:0.0:0.2928	.	30;30;30;30;30;30;30	E7ETR2;E7EMP0;Q5YLB2;P38398-3;Q6IN79;E9PFC7;P38398	.;.;.;.;.;.;BRCA1_HUMAN	F	30	ENSP00000350283:L30F;ENSP00000397145:L30F;ENSP00000326002:L30F;ENSP00000312236:L30F;ENSP00000246907:L30F;ENSP00000338007:L30F;ENSP00000417148:L30F;ENSP00000418960:L30F;ENSP00000420705:L30F;ENSP00000420412:L30F;ENSP00000419274:L30F;ENSP00000419988:L30F;ENSP00000419103:L30F;ENSP00000417554:L30F;ENSP00000420781:L30F	ENSP00000246907:L30F	L	-	3	2	BRCA1	38521313	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.682000	0.37628	0.143000	0.18926	-0.150000	0.13652	TTG		0.343	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2		NM_007294	
C2orf43	60526	hgsc.bcm.edu;ucsc.edu	37	2	20990106	20990106	+	Silent	SNP	A	A	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr2:20990106A>T	ENST00000237822.3	-	3	286	c.207T>A	c.(205-207)tcT>tcA	p.S69S	C2orf43_ENST00000381090.3_Silent_p.S69S|C2orf43_ENST00000440866.2_Silent_p.S69S|C2orf43_ENST00000435420.2_Intron|C2orf43_ENST00000541941.1_5'UTR|C2orf43_ENST00000419825.2_Silent_p.S69S|C2orf43_ENST00000403006.2_5'UTR	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	69										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTTGTCAAAGAGTATAAAG	0.408																																																	0													85.0	87.0	86.0					2																	20990106		2203	4300	6503	SO:0001819	synonymous_variant	60526			AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.207T>A	2.37:g.20990106A>T		Somatic		WXS	SOLID	Phase_I	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Silent	SNP	ENST00000237822.3	37	CCDS1702.1																																																																																				0.408	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1		NM_021925	
C3orf36	80111	hgsc.bcm.edu	37	3	133647487	133647487	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr3:133647487C>T	ENST00000408895.2	-	1	1169	c.161G>A	c.(160-162)aGg>aAg	p.R54K		NM_025041.2	NP_079317.2	Q3SXR2	CC036_HUMAN	chromosome 3 open reading frame 36	54										breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6						GAATGCCTTCCTGAGCGTGGT	0.652																																																	0													39.0	41.0	41.0					3																	133647487		2203	4300	6503	SO:0001583	missense	80111			AK025826	CCDS3083.1	3q22.1	2011-09-30			ENSG00000221972	ENSG00000221972			26170	protein-coding gene	gene with protein product						12477932	Standard	NM_025041		Approved	FLJ22173	uc003epz.1	Q3SXR2		ENST00000408895.2:c.161G>A	3.37:g.133647487C>T	ENSP00000386219:p.Arg54Lys	Somatic		WXS	SOLID	Phase_I	Q3SXR3|Q9H6K8	Missense_Mutation	SNP	ENST00000408895.2	37	CCDS3083.1	.	.	.	.	.	.	.	.	.	.	C	9.617	1.132863	0.21041	.	.	ENSG00000221972	ENST00000408895	.	.	.	2.11	1.22	0.21188	.	.	.	.	.	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.33694	0.421	B	0.27796	0.083	T	0.16778	-1.0391	8	0.87932	D	0	.	4.5545	0.12130	0.0:0.8087:0.0:0.1913	.	54	Q3SXR2	CC036_HUMAN	K	54	.	ENSP00000386219:R54K	R	-	2	0	C3orf36	135130177	0.005000	0.15991	0.026000	0.17262	0.316000	0.28119	1.097000	0.30988	0.465000	0.27167	0.313000	0.20887	AGG		0.652	C3orf36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_025041	
CABIN1	23523	hgsc.bcm.edu	37	22	24434873	24434873	+	Silent	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr22:24434873C>A	ENST00000398319.2	+	4	559	c.174C>A	c.(172-174)gcC>gcA	p.A58A	CABIN1_ENST00000405822.2_Silent_p.A58A|CABIN1_ENST00000263119.5_Silent_p.A58A	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	58					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CTGCCAAAGCCTACCATGAGC	0.562																																																	0													94.0	86.0	89.0					22																	24434873		2203	4300	6503	SO:0001819	synonymous_variant	23523			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.174C>A	22.37:g.24434873C>A		Somatic		WXS	SOLID	Phase_I	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	37	CCDS13823.1																																																																																				0.562	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2		NM_012295	
CCDC108	255101	hgsc.bcm.edu	37	2	219892423	219892423	+	Silent	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr2:219892423A>G	ENST00000341552.5	-	13	2243	c.2160T>C	c.(2158-2160)ccT>ccC	p.P720P	CCDC108_ENST00000453220.1_Silent_p.P720P|CCDC108_ENST00000410037.1_Silent_p.P655P|CCDC108_ENST00000441968.1_Silent_p.P720P|CCDC108_ENST00000409865.3_Silent_p.P709P	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	720						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.P720P(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTTGGGGTGAGGCGGCTGGA	0.612																																																	1	Substitution - coding silent(1)	ovary(1)											80.0	81.0	81.0					2																	219892423		2203	4300	6503	SO:0001819	synonymous_variant	255101			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2160T>C	2.37:g.219892423A>G		Somatic		WXS	SOLID	Phase_I	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																				0.612	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4		NM_194302	
CCNB3	85417	hgsc.bcm.edu;ucsc.edu	37	X	50052672	50052672	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chrX:50052672G>A	ENST00000376042.1	+	6	1801	c.1503G>A	c.(1501-1503)atG>atA	p.M501I	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.M501I			Q8WWL7	CCNB3_HUMAN	cyclin B3	501					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					AGGGGACAATGTCCCACTTGA	0.423																																																	0													46.0	43.0	44.0					X																	50052672		2203	4300	6503	SO:0001583	missense	85417			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.1503G>A	X.37:g.50052672G>A	ENSP00000365210:p.Met501Ile	Somatic		WXS	SOLID	Phase_I	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	G	7.461	0.644668	0.14451	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.17691	2.26;2.26	3.38	1.6	0.23607	.	987.722000	0.00166	N	0.000000	T	0.15305	0.0369	L	0.39898	1.24	0.09310	N	1	B	0.16396	0.017	B	0.09377	0.004	T	0.19128	-1.0315	9	.	.	.	.	4.7819	0.13206	0.3007:0.0:0.6993:0.0	.	501	Q8WWL7	CCNB3_HUMAN	I	501	ENSP00000365210:M501I;ENSP00000276014:M501I	.	M	+	3	0	CCNB3	50069412	0.003000	0.15002	0.001000	0.08648	0.220000	0.24768	0.101000	0.15251	0.300000	0.22699	0.509000	0.49947	ATG		0.423	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			
CCR9	10803	hgsc.bcm.edu	37	3	45943248	45943248	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr3:45943248G>C	ENST00000357632.2	+	3	1148	c.968G>C	c.(967-969)aGa>aCa	p.R323T	Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Missense_Mutation_p.R311T|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000355983.2_Missense_Mutation_p.R311T|CCR9_ENST00000422395.1_3'UTR|LZTFL1_ENST00000536047.1_Intron	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	323					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.R323I(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		GTGGGTGAGAGATTCCGCCGG	0.522																																																	1	Substitution - Missense(1)	ovary(1)											107.0	100.0	103.0					3																	45943248		2203	4300	6503	SO:0001583	missense	10803			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.968G>C	3.37:g.45943248G>C	ENSP00000350256:p.Arg323Thr	Somatic		WXS	SOLID	Phase_I	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	37	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261979	0.59431	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.37411	1.2;1.2;1.2	4.96	3.13	0.36017	.	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	L	0.60455	1.87	0.47949	D	0.999556	D	0.63046	0.992	P	0.61477	0.889	T	0.49560	-0.8927	10	0.87932	D	0	.	9.0593	0.36425	0.2137:0.0:0.7863:0.0	.	323	P51686	CCR9_HUMAN	T	323;311;311	ENSP00000350256:R323T;ENSP00000379292:R311T;ENSP00000348260:R311T	ENSP00000348260:R311T	R	+	2	0	CCR9	45918252	1.000000	0.71417	0.983000	0.44433	0.969000	0.65631	3.324000	0.52022	2.289000	0.77006	0.563000	0.77884	AGA		0.522	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			
CDHR3	222256	hgsc.bcm.edu;ucsc.edu	37	7	105656408	105656408	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr7:105656408A>G	ENST00000317716.9	+	11	1443	c.1363A>G	c.(1363-1365)Aat>Gat	p.N455D	CDHR3_ENST00000478080.1_Missense_Mutation_p.N367D|CDHR3_ENST00000343407.5_Missense_Mutation_p.N174D|CDHR3_ENST00000542731.1_Missense_Mutation_p.N455D|CDHR3_ENST00000470188.1_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	455	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AAGCCCAGAAAATGAGTTTCC	0.358																																																	0													104.0	98.0	100.0					7																	105656408		1840	4094	5934	SO:0001583	missense	222256			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1363A>G	7.37:g.105656408A>G	ENSP00000325954:p.Asn455Asp	Somatic		WXS	SOLID	Phase_I	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269840	0.80469	.	.	ENSG00000128536	ENST00000542731;ENST00000343407;ENST00000317716;ENST00000478080;ENST00000466045	T;T;T;T;T	0.69040	-0.35;0.4;-0.37;-0.17;-0.17	5.46	4.31	0.51392	Cadherin (3);Cadherin-like (1);	0.070003	0.64402	N	0.000019	T	0.80401	0.4616	M	0.78049	2.395	0.34776	D	0.734225	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.997;0.996;0.996	D	0.86236	0.1640	10	0.87932	D	0	-27.3915	11.1833	0.48642	0.928:0.0:0.072:0.0	.	172;442;455;367	Q6ZTQ4-2;B3KYA0;Q6ZTQ4;B7Z8X2	.;.;CDHR3_HUMAN;.	D	455;174;455;367;213	ENSP00000439766:N455D;ENSP00000341510:N174D;ENSP00000325954:N455D;ENSP00000417771:N367D;ENSP00000419017:N213D	ENSP00000325954:N455D	N	+	1	0	CDHR3	105443644	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.450000	0.52957	0.919000	0.36945	0.533000	0.62120	AAT		0.358	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2		NM_152750	
CFB	629	hgsc.bcm.edu	37	6	31915778	31915778	+	Missense_Mutation	SNP	C	C	A	rs535291979		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr6:31915778C>A	ENST00000425368.2	+	6	1330	c.817C>A	c.(817-819)Ctg>Atg	p.L273M	CFB_ENST00000497841.1_3'UTR|CFB_ENST00000456570.1_Missense_Mutation_p.L775M|CFB_ENST00000556679.1_Missense_Mutation_p.L775M|CFB_ENST00000477310.1_Missense_Mutation_p.L624M	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	273	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						GAACATCTACCTGGTGCTAGA	0.517																																																	0													110.0	114.0	113.0					6																	31915778		2203	4300	6503	SO:0001583	missense	629			L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"""Complement system"""	1037	protein-coding gene	gene with protein product		138470	"""B-factor, properdin"""	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.817C>A	6.37:g.31915778C>A	ENSP00000416561:p.Leu273Met	Somatic		WXS	SOLID	Phase_I	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.244179	0.59103	.	.	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4	5.14	2.28	0.28536	von Willebrand factor, type A (3);	0.542686	0.15485	N	0.259883	T	0.72630	0.3484	L	0.49350	1.555	0.31875	N	0.619229	D;B;P	0.53312	0.959;0.042;0.583	P;B;B	0.52267	0.694;0.146;0.19	T	0.67511	-0.5652	10	0.48119	T	0.1	-5.9482	12.2031	0.54337	0.5977:0.4023:0.0:0.0	.	775;273;273	B4E1Z4;P00751;P00751-2	.;CFAB_HUMAN;.	M	775;273;775;624	ENSP00000451848:L775M;ENSP00000416561:L273M;ENSP00000410815:L775M;ENSP00000418996:L624M	ENSP00000416561:L273M	L	+	1	2	CFB;XXbac-BPG116M5.17	32023757	0.987000	0.35691	1.000000	0.80357	0.997000	0.91878	0.001000	0.13038	0.291000	0.22468	0.561000	0.74099	CTG		0.517	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3		NM_001710	
CDK19	23097	hgsc.bcm.edu	37	6	111136336	111136336	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr6:111136336C>A	ENST00000368911.3	-	1	183	c.4G>T	c.(4-6)Gat>Tat	p.D2Y	CDK19_ENST00000323817.3_Intron|CDK19_ENST00000497709.1_Intron	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	2							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.D2N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						AAATCATAATCCATTGTCTGC	0.647																																																	1	Substitution - Missense(1)	ovary(1)											72.0	71.0	71.0					6																	111136336		2203	4300	6503	SO:0001583	missense	23097			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"""Cyclin-dependent kinases"""	19338	protein-coding gene	gene with protein product		614720	"""cyclin-dependent kinase (CDC2-like) 11"", ""cell division cycle 2-like 6 (CDK8-like)"""	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.4G>T	6.37:g.111136336C>A	ENSP00000357907:p.Asp2Tyr	Somatic		WXS	SOLID	Phase_I	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502754	0.85176	.	.	ENSG00000155111	ENST00000368911	T	0.65364	-0.15	3.41	3.41	0.39046	.	0.130621	0.48286	D	0.000192	T	0.74642	0.3743	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.80167	-0.1495	10	0.87932	D	0	-13.0957	14.135	0.65281	0.0:1.0:0.0:0.0	.	2	Q9BWU1	CDK19_HUMAN	Y	2	ENSP00000357907:D2Y	ENSP00000357907:D2Y	D	-	1	0	CDK19	111243029	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.570000	0.73996	1.909000	0.55274	0.550000	0.68814	GAT		0.647	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1		NM_015076	
COG1	9382	hgsc.bcm.edu	37	17	71196785	71196785	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr17:71196785A>G	ENST00000299886.4	+	6	1231	c.1151A>G	c.(1150-1152)gAc>gGc	p.D384G		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	384					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GGAATCCGGGACGCCATGTGG	0.498																																																	0													112.0	105.0	107.0					17																	71196785		2203	4300	6503	SO:0001583	missense	9382				CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1151A>G	17.37:g.71196785A>G	ENSP00000299886:p.Asp384Gly	Somatic		WXS	SOLID	Phase_I	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.891741	0.33442	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.25912	1.77;1.77	5.53	5.53	0.82687	.	0.096908	0.64402	D	0.000002	T	0.51669	0.1688	M	0.77616	2.38	0.80722	D	1	D;P;D	0.89917	1.0;0.941;1.0	D;P;D	0.72338	0.977;0.505;0.977	T	0.51293	-0.8724	10	0.37606	T	0.19	-25.3942	15.6586	0.77162	1.0:0.0:0.0:0.0	.	384;384;384	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	G	384	ENSP00000400111:D384G;ENSP00000299886:D384G	ENSP00000299886:D384G	D	+	2	0	COG1	68708380	1.000000	0.71417	0.184000	0.23157	0.421000	0.31385	8.792000	0.91856	2.102000	0.63906	0.460000	0.39030	GAC		0.498	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			
CSF1R	1436	hgsc.bcm.edu	37	5	149436911	149436911	+	Missense_Mutation	SNP	C	C	A	rs560352241	byFrequency	TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr5:149436911C>A	ENST00000286301.3	-	17	2549	c.2258G>T	c.(2257-2259)cGg>cTg	p.R753L	CSF1R_ENST00000515239.1_5'Flank	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	753	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.R753Q(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	AAGCAGGTCCCGGAGCTCCAG	0.647																																																	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)											55.0	47.0	50.0					5																	149436911		2203	4300	6503	SO:0001583	missense	1436			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.2258G>T	5.37:g.149436911C>A	ENSP00000286301:p.Arg753Leu	Somatic		WXS	SOLID	Phase_I	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	C	0.398	-0.919796	0.02396	.	.	ENSG00000182578	ENST00000286301	D	0.82526	-1.62	5.42	1.66	0.24008	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	1.175670	0.06268	N	0.695160	T	0.67674	0.2918	N	0.17379	0.485	0.18873	N	0.999987	B	0.22746	0.074	B	0.23419	0.046	T	0.52185	-0.8609	10	0.10902	T	0.67	.	5.1848	0.15178	0.0:0.3747:0.1596:0.4657	.	753	P07333	CSF1R_HUMAN	L	753	ENSP00000286301:R753L	ENSP00000286301:R753L	R	-	2	0	CSF1R	149417104	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	1.117000	0.31234	0.275000	0.22094	-0.258000	0.10820	CGG		0.647	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2		NM_005211	
CWC25	54883	hgsc.bcm.edu	37	17	36959026	36959026	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr17:36959026T>C	ENST00000225428.5	-	9	1387	c.1090A>G	c.(1090-1092)Aag>Gag	p.K364E	PIP4K2B_ENST00000269554.3_5'Flank|CWC25_ENST00000536127.1_Missense_Mutation_p.K301E	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	364										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						GCATGCCTCTTGAGGATGTTC	0.517																																																	0													196.0	200.0	199.0					17																	36959026		2011	4177	6188	SO:0001583	missense	54883			AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"""coiled-coil domain containing 49"""	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.1090A>G	17.37:g.36959026T>C	ENSP00000225428:p.Lys364Glu	Somatic		WXS	SOLID	Phase_I	A0JLM3|Q68DK5	Missense_Mutation	SNP	ENST00000225428.5	37	CCDS45663.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321099	0.41096	.	.	ENSG00000108296	ENST00000225428;ENST00000536127	.	.	.	5.71	2.18	0.27775	.	0.291903	0.42548	N	0.000688	T	0.48277	0.1491	M	0.63843	1.955	0.40942	D	0.984474	B;B	0.24258	0.1;0.1	B;B	0.23852	0.049;0.03	T	0.28586	-1.0039	9	0.21014	T	0.42	.	7.2386	0.26084	0.0:0.0726:0.2768:0.6505	.	301;364	B4DJK2;Q9NXE8	.;CWC25_HUMAN	E	364;301	.	ENSP00000225428:K364E	K	-	1	0	CWC25	34212552	0.990000	0.36364	0.773000	0.31616	0.423000	0.31445	0.705000	0.25675	0.086000	0.17137	0.533000	0.62120	AAG		0.517	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6		NM_017748	
DAPK3	1613	hgsc.bcm.edu	37	19	3964716	3964716	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr19:3964716C>T	ENST00000545797.2	-	3	579	c.336G>A	c.(334-336)acG>acA	p.T112T	DAPK3_ENST00000301264.3_Silent_p.T112T			O43293	DAPK3_HUMAN	death-associated protein kinase 3	112	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> M (in a colorectal adenocarcinoma sample; somatic mutation; greatly reduces kinase acivity, increases cell proliferation and cell survival). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21487036}.		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCGTCCTCCGTCAGCGACT	0.587																																																	0													111.0	109.0	110.0					19																	3964716		2203	4300	6503	SO:0001819	synonymous_variant	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.336G>A	19.37:g.3964716C>T		Somatic		WXS	SOLID	Phase_I	A0AVN4|B3KQE2|Q05JY4	Silent	SNP	ENST00000545797.2	37	CCDS12116.1																																																																																				0.587	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2		NM_001348	
DKK2	27123	hgsc.bcm.edu	37	4	107846995	107846995	+	Silent	SNP	G	G	T	rs528677483		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr4:107846995G>T	ENST00000285311.3	-	2	1039	c.334C>A	c.(334-336)Cga>Aga	p.R112R	DKK2_ENST00000513208.1_Silent_p.R12R|DKK2_ENST00000510463.1_Silent_p.R66R	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	112	DKK-type Cys-1.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R112*(1)|p.R112G(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ATGCCATCTCGGTGGCAGCGC	0.493																																																	2	Substitution - Nonsense(1)|Substitution - Missense(1)	ovary(1)|lung(1)											177.0	162.0	167.0					4																	107846995		2203	4300	6503	SO:0001819	synonymous_variant	27123			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.334C>A	4.37:g.107846995G>T		Somatic		WXS	SOLID	Phase_I	A0AVE9|B2R6S7|Q9UIU3	Silent	SNP	ENST00000285311.3	37	CCDS3675.1																																																																																				0.493	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			
DNMT3A	1788	hgsc.bcm.edu	37	2	25498413	25498413	+	Splice_Site	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr2:25498413C>T	ENST00000264709.3	-	5	786		c.e5-1		DNMT3A_ENST00000321117.5_Splice_Site	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTCTTTGCCTGTGGAGAGG	0.557			"""Mis, F, N, S"""		AML																																			Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0													184.0	198.0	193.0					2																	25498413		2203	4300	6503	SO:0001630	splice_region_variant	1788				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.449-1G>A	2.37:g.25498413C>T		Somatic		WXS	SOLID	Phase_I	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Splice_Site	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033320	0.75504	.	.	ENSG00000119772	ENST00000321117;ENST00000264709	.	.	.	4.63	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0066	0.58707	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNMT3A	25351917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.098000	0.57748	2.116000	0.64780	0.561000	0.74099	.		0.557	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1		NM_022552	Intron
EIF5	1983	hgsc.bcm.edu	37	14	103803541	103803541	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr14:103803541C>A	ENST00000216554.3	+	6	1092	c.416C>A	c.(415-417)aCa>aAa	p.T139K	SNORA28_ENST00000606769.1_RNA|EIF5_ENST00000560200.1_3'UTR|EIF5_ENST00000392715.2_Missense_Mutation_p.T139K|EIF5_ENST00000558506.1_Missense_Mutation_p.T139K	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	139					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(3)|kidney(2)|large_intestine(3)|lung(5)|pancreas(2)|skin(2)|upper_aerodigestive_tract(1)	18		Melanoma(154;0.155)	Epithelial(46;0.182)			AAACTCTGCACATTCATTCTC	0.383																																																	0													103.0	93.0	96.0					14																	103803541		2203	4300	6503	SO:0001583	missense	1983			U49436	CCDS9980.1	14q32.32	2006-05-11				ENSG00000100664			3299	protein-coding gene	gene with protein product		601710				8663286	Standard	NM_001969		Approved		uc001ymq.4	P55010		ENST00000216554.3:c.416C>A	14.37:g.103803541C>A	ENSP00000216554:p.Thr139Lys	Somatic		WXS	SOLID	Phase_I	Q53XB3|Q9H5N2|Q9UG48	Missense_Mutation	SNP	ENST00000216554.3	37	CCDS9980.1	.	.	.	.	.	.	.	.	.	.	.	24.7	4.564281	0.86335	.	.	ENSG00000100664	ENST00000216554;ENST00000392715	D;D	0.84370	-1.84;-1.84	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.88153	0.6360	M	0.86178	2.8	0.80722	D	1	B	0.28208	0.203	B	0.24394	0.053	D	0.85626	0.1267	10	0.87932	D	0	-18.3161	20.8598	0.99761	0.0:1.0:0.0:0.0	.	139	P55010	IF5_HUMAN	K	139	ENSP00000216554:T139K;ENSP00000376477:T139K	ENSP00000216554:T139K	T	+	2	0	EIF5	102873294	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.436000	0.80404	2.937000	0.99478	0.650000	0.86243	ACA		0.383	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2		NM_001969	
EPHA1	2041	hgsc.bcm.edu	37	7	143094667	143094667	+	Missense_Mutation	SNP	C	C	T	rs555414886		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr7:143094667C>T	ENST00000275815.3	-	9	1785	c.1699G>A	c.(1699-1701)Gtt>Att	p.V567I		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	567					activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.V567I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GACCGGAAAACGAGAATCCCA	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	ovary(1)											81.0	78.0	79.0					7																	143094667		2203	4300	6503	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1699G>A	7.37:g.143094667C>T	ENSP00000275815:p.Val567Ile	Somatic		WXS	SOLID	Phase_I	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	C	0.038	-1.299078	0.01364	.	.	ENSG00000146904	ENST00000275815	T	0.09538	2.97	5.72	-4.79	0.03200	.	1.179830	0.06167	N	0.676995	T	0.03477	0.0100	N	0.10916	0.065	0.09310	N	0.999999	B	0.09022	0.002	B	0.01281	0.0	T	0.39643	-0.9604	10	0.06236	T	0.91	.	1.2298	0.01941	0.3618:0.1989:0.0893:0.35	.	567	P21709	EPHA1_HUMAN	I	567	ENSP00000275815:V567I	ENSP00000275815:V567I	V	-	1	0	EPHA1	142804789	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	-1.724000	0.01865	-1.007000	0.03408	0.655000	0.94253	GTT		0.612	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			
F2RL1	2150	hgsc.bcm.edu	37	5	76129109	76129109	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr5:76129109G>T	ENST00000296677.4	+	2	883	c.677G>T	c.(676-678)tGt>tTt	p.C226F		NM_005242.4	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	226					blood coagulation (GO:0007596)|chemokine (C-C motif) ligand 2 secretion (GO:0035926)|chemokine secretion (GO:0090195)|defense response to virus (GO:0051607)|establishment of endothelial barrier (GO:0061028)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|interleukin-1 beta secretion (GO:0050702)|interleukin-10 secretion (GO:0072608)|leukocyte migration (GO:0050900)|leukocyte proliferation (GO:0070661)|mature dendritic cell differentiation (GO:0097029)|negative regulation of chemokine secretion (GO:0090198)|negative regulation of JNK cascade (GO:0046329)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neutrophil activation (GO:0042119)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of cell migration (GO:0030335)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of eosinophil degranulation (GO:0043311)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of neutrophil mediated killing of gram-negative bacterium (GO:0070963)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of blood coagulation (GO:0030193)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of JNK cascade (GO:0046328)|T cell activation involved in immune response (GO:0002286)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)	p.C226S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	13		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)		ATCACGACCTGTCATGATGTT	0.512																																																	1	Substitution - Missense(1)	central_nervous_system(1)											109.0	95.0	100.0					5																	76129109		2203	4300	6503	SO:0001583	missense	2150			BC018130	CCDS4033.1	5q13	2012-08-08			ENSG00000164251	ENSG00000164251		"""GPCR / Class A : Protease activated receptors"""	3538	protein-coding gene	gene with protein product	"""proteinase-activated receptor-2"""	600933		GPR11		7937743, 7556175	Standard	NM_005242		Approved	PAR2	uc003keo.3	P55085	OTTHUMG00000102118	ENST00000296677.4:c.677G>T	5.37:g.76129109G>T	ENSP00000296677:p.Cys226Phe	Somatic		WXS	SOLID	Phase_I	Q13317|Q13346|Q53XJ8	Missense_Mutation	SNP	ENST00000296677.4	37	CCDS4033.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383439	0.82792	.	.	ENSG00000164251	ENST00000296677	T	0.62639	0.01	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86777	0.6014	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90337	0.4356	9	.	.	.	-22.8925	19.9067	0.97010	0.0:0.0:1.0:0.0	.	226	P55085	PAR2_HUMAN	F	226	ENSP00000296677:C226F	.	C	+	2	0	F2RL1	76164865	1.000000	0.71417	0.996000	0.52242	0.920000	0.55202	9.808000	0.99193	2.703000	0.92315	0.655000	0.94253	TGT		0.512	F2RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219957.2			
FAM161B	145483	hgsc.bcm.edu	37	14	74411261	74411261	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr14:74411261C>T	ENST00000534936.1	-	3	807	c.702G>A	c.(700-702)atG>atA	p.M234I	FAM161B_ENST00000286544.3_Missense_Mutation_p.M297I			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	234										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CGCTGCGCTCCATGATCTCTT	0.617																																																	0													50.0	51.0	50.0					14																	74411261		2203	4300	6503	SO:0001583	missense	145483			AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.702G>A	14.37:g.74411261C>T	ENSP00000445326:p.Met234Ile	Somatic		WXS	SOLID	Phase_I	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	37		.	.	.	.	.	.	.	.	.	.	C	19.43	3.825375	0.71143	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.24151	1.87;1.87	5.26	5.26	0.73747	.	0.418350	0.24859	N	0.035038	T	0.29061	0.0722	L	0.58669	1.825	0.58432	D	0.999996	P	0.34462	0.454	B	0.31016	0.123	T	0.05007	-1.0912	10	0.40728	T	0.16	-1.2262	19.0716	0.93140	0.0:1.0:0.0:0.0	.	234	Q96MY7	F161B_HUMAN	I	297;234	ENSP00000286544:M297I;ENSP00000445326:M234I	ENSP00000286544:M297I	M	-	3	0	FAM161B	73481014	0.973000	0.33851	1.000000	0.80357	0.977000	0.68977	0.924000	0.28777	2.735000	0.93741	0.563000	0.77884	ATG		0.617	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_152445	
FLT1	2321	hgsc.bcm.edu	37	13	28919683	28919683	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr13:28919683A>G	ENST00000282397.4	-	16	2505	c.2254T>C	c.(2254-2256)Tcg>Ccg	p.S752P	FLT1_ENST00000540678.1_5'UTR	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	752					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GACTTGTCCGAGGTTCCTGGA	0.408																																																	0													50.0	50.0	50.0					13																	28919683		2203	4300	6503	SO:0001583	missense	2321			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2254T>C	13.37:g.28919683A>G	ENSP00000282397:p.Ser752Pro	Somatic		WXS	SOLID	Phase_I	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.379930	0.24944	.	.	ENSG00000102755	ENST00000282397	T	0.75821	-0.97	5.52	3.08	0.35506	.	0.593958	0.17196	N	0.183329	T	0.56572	0.1994	N	0.22421	0.69	0.09310	N	1	B	0.16166	0.016	B	0.13407	0.009	T	0.39961	-0.9588	10	0.24483	T	0.36	.	7.9166	0.29822	0.5338:0.3952:0.071:0.0	.	752	P17948	VGFR1_HUMAN	P	752	ENSP00000282397:S752P	ENSP00000282397:S752P	S	-	1	0	FLT1	27817683	0.001000	0.12720	0.999000	0.59377	0.887000	0.51463	0.203000	0.17315	0.900000	0.36469	0.454000	0.30748	TCG		0.408	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			
FOXJ3	22887	hgsc.bcm.edu	37	1	42693624	42693624	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr1:42693624G>A	ENST00000372572.1	-	7	769	c.458C>T	c.(457-459)gCa>gTa	p.A153V	FOXJ3_ENST00000361776.1_Missense_Mutation_p.A153V|FOXJ3_ENST00000372573.1_Missense_Mutation_p.A153V|FOXJ3_ENST00000545068.1_Missense_Mutation_p.A153V|FOXJ3_ENST00000361346.1_Missense_Mutation_p.A153V	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	153					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGTGTCTATTGCCCAGTAGGA	0.378																																																	0													85.0	77.0	79.0					1																	42693624		2203	4300	6503	SO:0001583	missense	22887			AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"""Forkhead boxes"""	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.458C>T	1.37:g.42693624G>A	ENSP00000361653:p.Ala153Val	Somatic		WXS	SOLID	Phase_I	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	37	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.415428	0.83449	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886	D;D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.68	5.68	0.88126	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.058247	0.64402	D	0.000004	D	0.96197	0.8760	L	0.38175	1.15	0.80722	D	1	P;D	0.71674	0.851;0.998	B;D	0.69142	0.372;0.962	D	0.96749	0.9552	10	0.87932	D	0	.	17.2843	0.87137	0.0:0.0:1.0:0.0	.	153;153	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	V	153	ENSP00000361654:A153V;ENSP00000361653:A153V;ENSP00000354620:A153V;ENSP00000354449:A153V;ENSP00000439044:A153V;ENSP00000393408:A153V	ENSP00000354620:A153V	A	-	2	0	FOXJ3	42466211	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.770000	0.85390	2.666000	0.90696	0.655000	0.94253	GCA		0.378	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1		NM_014947	
GAGE10	643832	hgsc.bcm.edu	37	X	49173729	49173729	+	Missense_Mutation	SNP	G	G	A	rs199839509		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chrX:49173729G>A	ENST00000407599.3	+	4	383	c.290G>A	c.(289-291)gGc>gAc	p.G97D		NM_001098413.2	NP_001091883.2	A6NGK3	GAG10_HUMAN	G antigen 10	97										breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	Ovarian(276;0.236)					CAGGAGATGGGCCTGCCAAAT	0.483																																																	0													141.0	141.0	141.0					X																	49173729		2202	4300	6502	SO:0001583	missense	643832					Xp11.23	2010-06-03			ENSG00000215274	ENSG00000215274			30968	protein-coding gene	gene with protein product							Standard	XM_006710256		Approved	OTTHUMG00000024136	uc010nir.1	A6NGK3	OTTHUMG00000024136	ENST00000407599.3:c.290G>A	X.37:g.49173729G>A	ENSP00000385415:p.Gly97Asp	Somatic		WXS	SOLID	Phase_I		Missense_Mutation	SNP	ENST00000407599.3	37	CCDS43938.1	.	.	.	.	.	.	.	.	.	.	.	0.086	-1.175531	0.01646	.	.	ENSG00000215274	ENST00000407599	T	0.08807	3.05	1.62	-2.74	0.05932	.	.	.	.	.	T	0.03011	0.0089	N	0.04959	-0.14	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.43718	-0.9374	9	0.22706	T	0.39	.	3.3124	0.07021	0.4939:0.2215:0.2845:0.0	.	97	A6NGK3	GAG10_HUMAN	D	97	ENSP00000385415:G97D	ENSP00000385415:G97D	G	+	2	0	GAGE10	49060673	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.836000	0.01690	-1.172000	0.02762	-0.571000	0.04153	GGC		0.483	GAGE10-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060816.1		NM_001098413	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629146	32629146	+	Silent	SNP	G	G	A	rs3210168	byFrequency	TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr6:32629146G>A	ENST00000399084.1	-	5	928	c.750C>T	c.(748-750)atC>atT	p.I250I	HLA-DQB1_ENST00000374943.4_Silent_p.I250I|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Silent_p.I250I|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	250					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TTTGACGGATGATAAGGCCCA	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1257	0.250998	0.1536	0.4078	5008	,	,		12457	0.3294		0.2396	False		,,,				2504	0.2025				Esophageal Squamous(151;720 1825 15000 40336 43415)												0								A		176,3772		2,172,1800	32.0	29.0	30.0		750	3.1	0.0	6	dbSNP_132	30	451,7403		4,443,3480	no	coding-synonymous	HLA-DQB1	NM_002123.4		6,615,5280	AA,AG,GG		5.7423,4.458,5.3127		250/262	32629146	627,11175	1974	3927	5901	SO:0001819	synonymous_variant	3119	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.750C>T	6.37:g.32629146G>A		Somatic		WXS	SOLID	Phase_I	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																				0.552	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1		NM_002123	
HMG20A	10363	hgsc.bcm.edu	37	15	77756618	77756618	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr15:77756618C>T	ENST00000381714.3	+	4	554	c.126C>T	c.(124-126)gcC>gcT	p.A42A	HMG20A_ENST00000336216.4_Silent_p.A42A	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	42					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GTAGTGGCGCCACATCATCCA	0.428																																																	0													141.0	119.0	126.0					15																	77756618		2196	4294	6490	SO:0001819	synonymous_variant	10363			AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"""High mobility group / Non-canonical"""	5001	protein-coding gene	gene with protein product	"""HMG box domain containing 1"""	605534	"""high-mobility group 20A"""			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.126C>T	15.37:g.77756618C>T		Somatic		WXS	SOLID	Phase_I	A6NHY3|D3DW78|Q53G31|Q9NSF6	Silent	SNP	ENST00000381714.3	37	CCDS10295.1																																																																																				0.428	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2		NM_018200	
ITGB3	3690	hgsc.bcm.edu	37	17	45369718	45369719	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr17:45369718_45369719insG	ENST00000559488.1	+	10	1490_1491	c.1474_1475insG	c.(1474-1476)tggfs	p.W492fs	ITGB3_ENST00000435993.2_Frame_Shift_Ins_p.W445fs|ITGB3_ENST00000560629.1_Frame_Shift_Ins_p.A481fs	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	492	Cysteine-rich tandem repeats.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TGGGCCTGGCTGGCTGGGATCC	0.624																																																	0																																										SO:0001589	frameshift_variant	3690				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1476dupG	17.37:g.45369720_45369720dupG	ENSP00000452786:p.Trp492fs	Somatic		WXS	SOLID	Phase_I	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Frame_Shift_Ins	INS	ENST00000559488.1	37	CCDS11511.1																																																																																				0.624	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3		NM_000212	
ITPR2	3709	hgsc.bcm.edu	37	12	26784955	26784955	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr12:26784955C>T	ENST00000381340.3	-	22	3194	c.2778G>A	c.(2776-2778)gaG>gaA	p.E926E	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	926					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.E926E(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGGTCATCATCTCTCCCACCC	0.527																																																	1	Substitution - coding silent(1)	kidney(1)											114.0	118.0	116.0					12																	26784955		2066	4206	6272	SO:0001819	synonymous_variant	3709			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2778G>A	12.37:g.26784955C>T		Somatic		WXS	SOLID	Phase_I	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																				0.527	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1		NM_002223	
JAK2	3717	hgsc.bcm.edu	37	9	5072516	5072516	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:5072516T>C	ENST00000381652.3	+	13	2160	c.1666T>C	c.(1666-1668)Ttt>Ctt	p.F556L	JAK2_ENST00000539801.1_Missense_Mutation_p.F556L|JAK2_ENST00000544510.1_Missense_Mutation_p.F407L	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	556	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCAAGGCACTTTTACAAAGAT	0.358		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																															Dom	yes		9	9p24	3717	Janus kinase 2		L	0													53.0	54.0	54.0					9																	5072516		2203	4300	6503	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1666T>C	9.37:g.5072516T>C	ENSP00000371067:p.Phe556Leu	Somatic		WXS	SOLID	Phase_I	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.867611	0.91587	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.89196	-2.48;-2.48;-2.48	5.73	5.73	0.89815	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.96281	0.8787	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96799	0.9588	10	0.45353	T	0.12	-18.4828	16.0085	0.80380	0.0:0.0:0.0:1.0	.	556	O60674	JAK2_HUMAN	L	556;556;407	ENSP00000440387:F556L;ENSP00000371067:F556L;ENSP00000443103:F407L	ENSP00000371067:F556L	F	+	1	0	JAK2	5062516	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.685000	0.84117	2.185000	0.69588	0.477000	0.44152	TTT		0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			
JAK2	3717	hgsc.bcm.edu	37	9	5072560	5072560	+	Silent	SNP	C	C	T	rs146433914	byFrequency	TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:5072560C>T	ENST00000381652.3	+	13	2204	c.1710C>T	c.(1708-1710)taC>taT	p.Y570Y	JAK2_ENST00000539801.1_Silent_p.Y570Y|JAK2_ENST00000544510.1_Silent_p.Y421Y	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	570	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.Y570Y(4)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TAGGAGACTACGGTCAACTGC	0.348		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				C|||	3	0.000599042	0.0	0.0029	5008	,	,		18072	0.0		0.001	False		,,,				2504	0.0							Dom	yes		9	9p24	3717	Janus kinase 2		L	4	Substitution - coding silent(4)	haematopoietic_and_lymphoid_tissue(4)						C		0,4406		0,0,2203	69.0	71.0	70.0		1710	0.8	1.0	9	dbSNP_134	70	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	JAK2	NM_004972.3		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		570/1133	5072560	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1710C>T	9.37:g.5072560C>T		Somatic		WXS	SOLID	Phase_I	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			
LDLR	3949	hgsc.bcm.edu;ucsc.edu	37	19	11217289	11217289	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr19:11217289G>A	ENST00000558518.1	+	5	930	c.743G>A	c.(742-744)tGc>tAc	p.C248Y	LDLR_ENST00000558013.1_Missense_Mutation_p.C248Y|LDLR_ENST00000545707.1_Missense_Mutation_p.C121Y|LDLR_ENST00000557933.1_Missense_Mutation_p.C248Y|LDLR_ENST00000535915.1_Missense_Mutation_p.C207Y|LDLR_ENST00000455727.2_Intron	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	248	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.		C -> F (in Bretagne-1).|C -> Y (in FH; British patient). {ECO:0000269|PubMed:9026534}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GATGGAAACTGCATCCATGGC	0.522																																					GBM(18;201 575 7820 21545)												1	Unknown(1)	lung(1)	GRCh37	CM920428|CM962656	LDLR	M							136.0	121.0	126.0					19																	11217289		2203	4300	6503	SO:0001583	missense	3949			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.743G>A	19.37:g.11217289G>A	ENSP00000454071:p.Cys248Tyr	Somatic		WXS	SOLID	Phase_I	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200819	0.58234	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915	D;D	0.99919	-8.0;-8.0	5.1	5.1	0.69264	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000007	D	0.99949	0.9978	H	0.97983	4.12	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.984;0.991	D;D;D;D;D	0.97110	1.0;1.0;0.99;0.99;0.99	D	0.95966	0.8966	10	0.87932	D	0	.	17.2847	0.87138	0.0:0.0:1.0:0.0	.	121;127;207;260;248	B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;LDLR_HUMAN	Y	248;121;207	ENSP00000437639:C121Y;ENSP00000440520:C207Y	ENSP00000252444:C248Y	C	+	2	0	LDLR	11078289	1.000000	0.71417	0.148000	0.22405	0.165000	0.22458	9.796000	0.99103	2.370000	0.80446	0.462000	0.41574	TGC		0.522	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			
LRRC19	64922	hgsc.bcm.edu;ucsc.edu	37	9	26995607	26995607	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:26995607A>T	ENST00000380055.5	-	5	1135	c.1025T>A	c.(1024-1026)tTt>tAt	p.F342Y	IFT74_ENST00000443698.1_Intron|IFT74_ENST00000380062.5_Intron|LRRC19_ENST00000482770.1_5'UTR|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	342						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		TAATTGTTCAAATATTACTGT	0.308																																																	0													105.0	107.0	106.0					9																	26995607		2203	4300	6503	SO:0001583	missense	64922			AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.1025T>A	9.37:g.26995607A>T	ENSP00000369395:p.Phe342Tyr	Somatic		WXS	SOLID	Phase_I	A0AV00|B9EG91	Missense_Mutation	SNP	ENST00000380055.5	37	CCDS6518.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.119894	0.77323	.	.	ENSG00000184434	ENST00000380055	T	0.56103	0.48	5.55	5.55	0.83447	.	0.210963	0.37857	N	0.001904	T	0.42494	0.1205	L	0.29908	0.895	0.36349	D	0.859974	P	0.48503	0.911	B	0.42282	0.382	T	0.57579	-0.7787	10	0.87932	D	0	-18.1003	11.4539	0.50169	0.8653:0.0:0.0:0.1347	.	342	Q9H756	LRC19_HUMAN	Y	342	ENSP00000369395:F342Y	ENSP00000369395:F342Y	F	-	2	0	LRRC19	26985607	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.364000	0.44187	2.115000	0.64714	0.477000	0.44152	TTT		0.308	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2		NM_022901	
MKL1	57591	hgsc.bcm.edu;ucsc.edu	37	22	40825689	40825689	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr22:40825689A>C	ENST00000355630.3	-	7	812	c.222T>G	c.(220-222)atT>atG	p.I74M	MKL1_ENST00000407029.1_Missense_Mutation_p.I74M|MKL1_ENST00000402630.1_Missense_Mutation_p.I74M|MKL1_ENST00000396617.3_Missense_Mutation_p.I74M|MKL1_ENST00000402042.1_Missense_Mutation_p.I74M	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	74	Mediates interaction with SCAI and ACTB. {ECO:0000250}.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GCCTCTGTGCAATCTTCTCAT	0.577			T	RBM15	acute megakaryocytic leukemia																																			Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	0													119.0	103.0	109.0					22																	40825689		2203	4300	6503	SO:0001583	missense	57591			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.222T>G	22.37:g.40825689A>C	ENSP00000347847:p.Ile74Met	Somatic		WXS	SOLID	Phase_I	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.119379	0.77323	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029;ENST00000402630	D;D;D;D;D	0.99871	-7.35;-7.35;-7.35;-7.35;-7.35	5.25	-5.05	0.02955	.	0.000000	0.85682	D	0.000000	D	0.99654	0.9872	M	0.69823	2.125	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.998;0.998	D	0.98621	1.0667	10	0.87932	D	0	-11.6657	10.1178	0.42601	0.3121:0.0:0.5412:0.1468	.	74;74;74	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	M	74	ENSP00000347847:I74M;ENSP00000379861:I74M;ENSP00000385584:I74M;ENSP00000385835:I74M;ENSP00000385076:I74M	ENSP00000347847:I74M	I	-	3	3	MKL1	39155635	0.937000	0.31787	0.928000	0.36995	0.993000	0.82548	0.071000	0.14594	-0.698000	0.05085	0.383000	0.25322	ATT		0.577	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1		NM_020831	
MTCH2	23788	hgsc.bcm.edu	37	11	47644274	47644274	+	Silent	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr11:47644274A>G	ENST00000302503.3	-	12	961	c.804T>C	c.(802-804)tgT>tgC	p.C268C	MTCH2_ENST00000534074.1_5'UTR|MTCH2_ENST00000542981.1_Silent_p.C120C	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	268					protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						GCATGCACCAACAGTCTATCC	0.313																																																	0													75.0	71.0	72.0					11																	47644274		2201	4298	6499	SO:0001819	synonymous_variant	23788			AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"""Solute carriers"""	17587	protein-coding gene	gene with protein product	"""solute carrier family 25, member 50"""	613221	"""mitochondrial carrier homolog 2 (C. elegans)"""				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.804T>C	11.37:g.47644274A>G		Somatic		WXS	SOLID	Phase_I	B2R7L8	Silent	SNP	ENST00000302503.3	37	CCDS7943.1																																																																																				0.313	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391921.2		NM_014342	
NAA15	80155	hgsc.bcm.edu	37	4	140280992	140280992	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr4:140280992C>T	ENST00000296543.5	+	12	1676	c.1353C>T	c.(1351-1353)taC>taT	p.Y451Y	NAA15_ENST00000398947.1_Silent_p.Y451Y	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	451					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.Y451*(1)		NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						GTGCAAAATACATGCTAAAAG	0.388																																																	1	Substitution - Nonsense(1)	ovary(1)											91.0	87.0	88.0					4																	140280992		1917	4158	6075	SO:0001819	synonymous_variant	80155			AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.1353C>T	4.37:g.140280992C>T		Somatic		WXS	SOLID	Phase_I	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Silent	SNP	ENST00000296543.5	37	CCDS43270.1																																																																																				0.388	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2		NM_057175	
NAIP	4671	hgsc.bcm.edu	37	5	70308462	70308462	+	Missense_Mutation	SNP	C	C	A	rs147757754		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr5:70308462C>A	ENST00000517649.1	-	4	571	c.281G>T	c.(280-282)gGg>gTg	p.G94V	NAIP_ENST00000194097.4_Missense_Mutation_p.G94V|NAIP_ENST00000503719.2_Intron|NAIP_ENST00000523981.1_Intron|NAIP_ENST00000508426.2_Missense_Mutation_p.G94V	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	94					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)	p.G94E(1)|p.G94A(1)		central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		GCACTGAATCCCAGATTTTAC	0.493																																																	2	Substitution - Missense(2)	lung(1)|skin(1)											80.0	73.0	75.0					5																	70308462		2202	4296	6498	SO:0001583	missense	4671			U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.281G>T	5.37:g.70308462C>A	ENSP00000428657:p.Gly94Val	Somatic		WXS	SOLID	Phase_I	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Missense_Mutation	SNP	ENST00000517649.1	37	CCDS4009.1	.	.	.	.	.	.	.	.	.	.	c	8.921	0.961070	0.18583	.	.	ENSG00000249437	ENST00000517649;ENST00000194097;ENST00000508426	T;T;T	0.71579	-0.58;-0.58;-0.58	3.26	2.33	0.28932	Baculoviral inhibition of apoptosis protein repeat (5);	0.515035	0.15663	U	0.250792	T	0.69314	0.3097	N	0.13272	0.32	0.18873	N	0.999989	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.971	T	0.60110	-0.7327	10	0.37606	T	0.19	.	11.0163	0.47691	0.0:0.6375:0.3625:0.0	.	94;94	E7EQW0;Q13075	.;BIRC1_HUMAN	V	94	ENSP00000428657:G94V;ENSP00000443944:G94V;ENSP00000429545:G94V	ENSP00000443944:G94V	G	-	2	0	NAIP	70344218	0.001000	0.12720	0.028000	0.17463	0.087000	0.18053	0.838000	0.27572	0.870000	0.35726	0.436000	0.28706	GGG		0.493	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6		NM_004536	
NALCN	259232	hgsc.bcm.edu	37	13	101714442	101714442	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr13:101714442G>A	ENST00000251127.6	-	41	4714	c.4633C>T	c.(4633-4635)Cgg>Tgg	p.R1545W	NALCN-AS1_ENST00000457843.1_RNA	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1545					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.R1545W(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AAGCTCTTCCGGATGTCCACG	0.537																																																	1	Substitution - Missense(1)	ovary(1)											84.0	64.0	71.0					13																	101714442		2203	4300	6503	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4633C>T	13.37:g.101714442G>A	ENSP00000251127:p.Arg1545Trp	Somatic		WXS	SOLID	Phase_I	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.058340	0.76074	.	.	ENSG00000102452	ENST00000251127	D	0.98012	-4.66	5.82	2.79	0.32731	.	0.000000	0.85682	D	0.000000	D	0.97895	0.9308	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.98276	1.0506	10	0.87932	D	0	.	13.6106	0.62076	0.0:0.0:0.4732:0.5268	.	1545	Q8IZF0	NALCN_HUMAN	W	1545	ENSP00000251127:R1545W	ENSP00000251127:R1545W	R	-	1	2	NALCN	100512443	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.261000	0.43276	1.407000	0.46875	0.650000	0.86243	CGG		0.537	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2		NM_052867	
NDUFA6	4700	hgsc.bcm.edu;ucsc.edu	37	22	42482291	42482291	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr22:42482291T>C	ENST00000498737.2	-	3	493	c.361A>G	c.(361-363)Aaa>Gaa	p.K121E	NDUFA6_ENST00000470753.1_Missense_Mutation_p.K38E|NDUFA6_ENST00000602404.1_Missense_Mutation_p.K95E	NM_002490.3	NP_002481.2	P56556	NDUA6_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa	121					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						TTCCATACTTTAATTGTTTCT	0.458																																																	0													189.0	167.0	175.0					22																	42482291		2203	4300	6503	SO:0001583	missense	4700			AF047182	CCDS33656.1	22q13.2	2010-05-07	2002-08-29		ENSG00000184983	ENSG00000184983		"""LYR motif containing"", ""Mitochondrial respiratory chain complex / Complex I"""	7690	protein-coding gene	gene with protein product	"""complex I B14 subunit"""	602138	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (14kD, B14)"""			9763676, 9425316	Standard	NM_002490		Approved	B14, LYRM6, CI-B14, NADHB14	uc003bcb.3	P56556	OTTHUMG00000151287	ENST00000498737.2:c.361A>G	22.37:g.42482291T>C	ENSP00000418842:p.Lys121Glu	Somatic		WXS	SOLID	Phase_I	B2RE54|O43675|Q6FGW0|Q6IBT8|Q6IC39	Missense_Mutation	SNP	ENST00000498737.2	37	CCDS33656.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.492141	0.44352	.	.	ENSG00000184983	ENST00000498737	T	0.63580	-0.05	6.17	4.02	0.46733	.	0.479918	0.27500	N	0.019087	T	0.45895	0.1365	N	0.24115	0.695	0.33284	D	0.562692	B	0.15930	0.015	B	0.12837	0.008	T	0.46938	-0.9155	10	0.14656	T	0.56	-0.4883	13.3636	0.60669	0.0:0.0:0.3739:0.6261	.	121	P56556	NDUA6_HUMAN	E	121	ENSP00000418842:K121E	ENSP00000418842:K121E	K	-	1	0	NDUFA6	40812237	0.659000	0.27411	0.094000	0.20943	0.953000	0.61014	0.343000	0.19944	0.534000	0.28695	0.533000	0.62120	AAA		0.458	NDUFA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322089.4		NM_002490	
OR4C3	256144	hgsc.bcm.edu	37	11	48346661	48346669	+	In_Frame_Del	DEL	TTGCTGATC	TTGCTGATC	-	rs201980031|rs138704181		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	TTGCTGATC	TTGCTGATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr11:48346661_48346669delTTGCTGATC	ENST00000319856.4	+	1	190_198	c.169_177delTTGCTGATC	c.(169-177)ttgctgatcdel	p.LLI57del		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TGTGGTCTTTTTGCTGATCTATGTGGTCA	0.469																																																	0										1956,2308		0,1956,176						-1.1	0.0		dbSNP_126	130	3671,4583		0,3671,456	no	coding	OR4C3	NM_001004702.1		0,5627,632	A1A1,A1R,RR		44.4754,45.8724,44.9513				5627,6891				SO:0001651	inframe_deletion	256144			AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"""GPCR / Class A : Olfactory receptors"""	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.169_177delTTGCTGATC	11.37:g.48346661_48346669delTTGCTGATC	ENSP00000321419:p.Leu57_Ile59del	Somatic		WXS	SOLID	Phase_I	B2RNF2|Q6IFB3	In_Frame_Del	DEL	ENST00000319856.4	37	CCDS31489.1																																																																																				0.469	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1		NM_001004702	
OTC	5009	hgsc.bcm.edu	37	X	38211976	38211976	+	Missense_Mutation	SNP	A	A	T	rs72552297		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chrX:38211976A>T	ENST00000039007.4	+	1	179	c.27A>T	c.(25-27)ttA>ttT	p.L9F	OTC_ENST00000488812.1_3'UTR|TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	9					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)	p.L9F(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	GGATCCTGTTAAACAATGCAG	0.418																																																	1	Substitution - Missense(1)	ovary(1)											155.0	127.0	136.0					X																	38211976		2202	4300	6502	SO:0001583	missense	5009			K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.27A>T	X.37:g.38211976A>T	ENSP00000039007:p.Leu9Phe	Somatic		WXS	SOLID	Phase_I	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	a	6.144	0.394849	0.11638	.	.	ENSG00000036473	ENST00000039007	D	0.99176	-5.52	5.77	1.97	0.26223	.	0.570391	0.17778	N	0.162330	D	0.93903	0.8049	N	0.08118	0	0.26399	N	0.976459	B	0.02656	0.0	B	0.01281	0.0	D	0.87494	0.2429	10	0.13470	T	0.59	-3.6709	5.8666	0.18779	0.1724:0.2911:0.5365:0.0	.	9	P00480	OTC_HUMAN	F	9	ENSP00000039007:L9F	ENSP00000039007:L9F	L	+	3	2	OTC	38096920	0.995000	0.38212	0.941000	0.38009	0.629000	0.37895	0.450000	0.21762	-0.033000	0.13736	-0.918000	0.02743	TTA		0.418	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			
PABPC1	26986	hgsc.bcm.edu	37	8	101721692	101721692	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr8:101721692G>A	ENST00000318607.5	-	8	2368	c.1240C>T	c.(1240-1242)Cca>Tca	p.P414S	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000522387.1_Missense_Mutation_p.P382S|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.P369S	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	414					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CCTACCTGTGGGATAGCTGCC	0.473																																																	0													93.0	84.0	87.0					8																	101721692		2203	4300	6503	SO:0001583	missense	26986			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1240C>T	8.37:g.101721692G>A	ENSP00000313007:p.Pro414Ser	Somatic		WXS	SOLID	Phase_I	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.40|17.40	3.380402|3.380402	0.61845|0.61845	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.35421	.|1.4;1.31;2.3	5.37|5.37	4.49|4.49	0.54785|0.54785	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000004|0.000004	T|T	0.47097|0.47097	0.1427|0.1427	M|M	0.86343|0.86343	2.81|2.81	0.58432|0.58432	D|D	0.999999|0.999999	.|B;B;B	.|0.17667	.|0.002;0.023;0.012	.|B;B;B	.|0.23275	.|0.045;0.045;0.014	T|T	0.52902|0.52902	-0.8513|-0.8513	6|10	.|0.72032	.|D	.|0.01	.|.	14.1037|14.1037	0.65075|0.65075	0.0725:0.0:0.9275:0.0|0.0725:0.0:0.9275:0.0	.|.	.|382;414;414	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	L|S	246|414;414;369;382	.|ENSP00000313007:P414S;ENSP00000429594:P369S;ENSP00000429395:P382S	.|ENSP00000313007:P414S	P|P	-|-	2|1	0|0	PABPC1|PABPC1	101790868|101790868	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.831000|9.831000	0.99420|0.99420	1.395000|1.395000	0.46643|0.46643	0.655000|0.655000	0.94253|0.94253	CCC|CCA		0.473	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1		NM_002568	
PANK4	55229	hgsc.bcm.edu;ucsc.edu	37	1	2443118	2443118	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr1:2443118G>A	ENST00000378466.3	-	14	1744	c.1732C>T	c.(1732-1734)Ctt>Ttt	p.L578F	PANK4_ENST00000435556.3_Missense_Mutation_p.L539F	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	578					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		TCGGATTCAAGGACACTGCAT	0.502																																																	0													101.0	86.0	91.0					1																	2443118		2202	4297	6499	SO:0001583	missense	55229			AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1732C>T	1.37:g.2443118G>A	ENSP00000367727:p.Leu578Phe	Somatic		WXS	SOLID	Phase_I	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352428	0.41700	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.07688	3.17;3.17	4.96	4.96	0.65561	Domain of unknown function DUF89 (2);	0.000000	0.85682	D	0.000000	T	0.09949	0.0244	L	0.41492	1.28	0.80722	D	1	P;P	0.42827	0.791;0.791	B;B	0.43155	0.41;0.41	T	0.27020	-1.0086	10	0.10902	T	0.67	-14.8608	17.1768	0.86844	0.0:0.0:1.0:0.0	.	539;578	E9PHT6;Q9NVE7	.;PANK4_HUMAN	F	578;539	ENSP00000367727:L578F;ENSP00000421433:L539F	ENSP00000367727:L578F	L	-	1	0	PANK4	2432978	1.000000	0.71417	0.951000	0.38953	0.297000	0.27493	8.502000	0.90505	2.299000	0.77371	0.462000	0.41574	CTT		0.502	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			
PIK3CA	5290	hgsc.bcm.edu;ucsc.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	Somatic		WXS	SOLID	Phase_I	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			
PRMT1	3276	hgsc.bcm.edu	37	19	50187293	50187293	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr19:50187293C>T	ENST00000391851.4	+	5	597	c.468C>T	c.(466-468)ctC>ctT	p.L156L	PRMT1_ENST00000532489.1_Silent_p.L128L|MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000454376.2_Silent_p.L174L	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	164	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.			DIIISEWMGYCLFYESMLNTVLYARDKWL -> ASSSASGW ATASSTSPCSTPCSMPGTSV (in Ref. 2; BAA11029). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		AGTCCATGCTCAACACCGTGC	0.612																																																	0													191.0	132.0	152.0					19																	50187293		2203	4300	6503	SO:0001819	synonymous_variant	3276			D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"""Protein arginine methyltransferases"""	5187	protein-coding gene	gene with protein product		602950	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2"", ""HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"""	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.468C>T	19.37:g.50187293C>T		Somatic		WXS	SOLID	Phase_I	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Silent	SNP	ENST00000391851.4	37	CCDS42592.1	.	.	.	.	.	.	.	.	.	.	C	7.009	0.556349	0.13436	.	.	ENSG00000126457	ENST00000524771	.	.	.	4.15	1.89	0.25635	.	.	.	.	.	T	0.61540	0.2355	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57100	-0.7869	4	.	.	.	-0.1749	11.8655	0.52490	0.0:0.4705:0.5295:0.0	.	.	.	.	L	184	.	.	S	+	2	0	PRMT1	54879105	0.958000	0.32768	1.000000	0.80357	0.677000	0.39632	0.127000	0.15790	0.338000	0.23692	0.591000	0.81541	TCA		0.612	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1		NM_001536	
PTPRA	5786	hgsc.bcm.edu	37	20	3016252	3016252	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr20:3016252C>A	ENST00000216877.6	+	20	2315	c.1915C>A	c.(1915-1917)Cca>Aca	p.P639T	PTPRA_ENST00000399903.2_Missense_Mutation_p.P648T|PTPRA_ENST00000318266.5_Missense_Mutation_p.P639T|PTPRA_ENST00000356147.3_Missense_Mutation_p.P639T|PTPRA_ENST00000358719.4_Missense_Mutation_p.P504T|PTPRA_ENST00000380393.3_Missense_Mutation_p.P648T|PTPRA_ENST00000425918.2_Missense_Mutation_p.P659T	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	648	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CCAGTACTGGCCATCTGATGG	0.547																																																	0													95.0	83.0	87.0					20																	3016252		2203	4300	6503	SO:0001583	missense	5786				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1915C>A	20.37:g.3016252C>A	ENSP00000216877:p.Pro639Thr	Somatic		WXS	SOLID	Phase_I	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.294636	0.81025	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	T;T;T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09;2.09;2.09	5.57	4.62	0.57501	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	U	0.000000	T	0.58119	0.2100	M	0.93898	3.47	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.958	T	0.72246	-0.4349	10	0.72032	D	0.01	.	16.5675	0.84602	0.0:0.8695:0.1305:0.0	.	659;648;639	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	T	648;639;648;504;258;659;639;639	ENSP00000369756:P648T;ENSP00000216877:P639T;ENSP00000382787:P648T;ENSP00000351559:P504T;ENSP00000393553:P659T;ENSP00000314568:P639T;ENSP00000348468:P639T	ENSP00000216877:P639T	P	+	1	0	PTPRA	2964252	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.037000	0.70956	1.328000	0.45358	0.563000	0.77884	CCA		0.547	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			
PTPRM	5797	hgsc.bcm.edu	37	18	7955227	7955227	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr18:7955227G>A	ENST00000332175.8	+	7	1984	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	PTPRM_ENST00000400053.4_Missense_Mutation_p.R254Q|PTPRM_ENST00000444013.1_Missense_Mutation_p.R103Q|PTPRM_ENST00000400060.4_Missense_Mutation_p.R316Q|PTPRM_ENST00000580170.1_Missense_Mutation_p.R316Q	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	316	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ATTGTGGCCCGAGAGGTGGAG	0.557																																																	0													50.0	48.0	49.0					18																	7955227		2203	4300	6503	SO:0001583	missense	5797			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.947G>A	18.37:g.7955227G>A	ENSP00000331418:p.Arg316Gln	Somatic		WXS	SOLID	Phase_I	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.948266	0.53186	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.053577	0.64402	D	0.000001	T	0.42494	0.1205	L	0.55103	1.725	0.44295	D	0.997162	P;P;P	0.50617	0.661;0.937;0.937	B;B;B	0.39971	0.152;0.315;0.315	T	0.27773	-1.0064	10	0.27785	T	0.31	.	13.7	0.62602	0.07:0.0:0.93:0.0	.	103;316;316	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	Q	316;316;254;103	ENSP00000331418:R316Q;ENSP00000382933:R316Q;ENSP00000382927:R254Q;ENSP00000387608:R103Q	ENSP00000331418:R316Q	R	+	2	0	PTPRM	7945227	0.998000	0.40836	0.966000	0.40874	0.947000	0.59692	6.510000	0.73729	2.865000	0.98341	0.655000	0.94253	CGA		0.557	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			
ROCK1	6093	hgsc.bcm.edu	37	18	18600158	18600158	+	Silent	SNP	G	G	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr18:18600158G>A	ENST00000399799.2	-	12	2255	c.1315C>T	c.(1315-1317)Ctg>Ttg	p.L439L		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	439	Interaction with FHOD1.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCATTATGCAGCTGTTCTTCC	0.264																																																	0													82.0	76.0	78.0					18																	18600158		2202	4288	6490	SO:0001819	synonymous_variant	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.1315C>T	18.37:g.18600158G>A		Somatic		WXS	SOLID	Phase_I	B0YJ91|Q2KHM4|Q59GZ4	Silent	SNP	ENST00000399799.2	37	CCDS11870.2																																																																																				0.264	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2		NM_005406	
SCYL1	57410	hgsc.bcm.edu	37	11	65303520	65303520	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr11:65303520C>T	ENST00000270176.5	+	11	1560	c.1483C>T	c.(1483-1485)Cac>Tac	p.H495Y	SCYL1_ENST00000420247.2_Missense_Mutation_p.H495Y|SCYL1_ENST00000527009.1_Missense_Mutation_p.H352Y|SCYL1_ENST00000533862.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000524944.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000525364.1_Missense_Mutation_p.H495Y|SCYL1_ENST00000279270.6_Missense_Mutation_p.H495Y	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	495			H -> Y (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)	p.H495Y(1)		ovary(1)|skin(1)	2						TGCTGCCACCCACAACCTCTA	0.592																																																	1	Substitution - Missense(1)	skin(1)											89.0	91.0	90.0					11																	65303520		1980	4152	6132	SO:0001583	missense	57410			AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1483C>T	11.37:g.65303520C>T	ENSP00000270176:p.His495Tyr	Somatic		WXS	SOLID	Phase_I	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	37	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.335543	0.24253	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (1);	0.104625	0.64402	D	0.000005	T	0.45915	0.1366	L	0.56769	1.78	0.80722	D	1	B;D;B;B;P	0.57571	0.038;0.98;0.232;0.232;0.928	B;P;B;B;P	0.54706	0.085;0.759;0.113;0.113;0.579	T	0.33369	-0.9871	10	0.49607	T	0.09	-11.242	16.7806	0.85562	0.0:1.0:0.0:0.0	.	495;495;495;495;495	E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;.;NTKL_HUMAN	Y	495;495;495;495;495;495;495;495;352	ENSP00000270176:H495Y;ENSP00000431635:H495Y;ENSP00000408192:H495Y;ENSP00000437254:H495Y;ENSP00000433450:H495Y;ENSP00000279270:H495Y;ENSP00000432175:H495Y;ENSP00000436993:H352Y	ENSP00000270176:H495Y	H	+	1	0	SCYL1	65060096	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.079000	0.64431	2.577000	0.86979	0.462000	0.41574	CAC		0.592	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2		NM_020680	
SFMBT2	57713	hgsc.bcm.edu	37	10	7239537	7239537	+	Silent	SNP	C	C	A	rs200717836		TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr10:7239537C>A	ENST00000361972.4	-	15	1761	c.1671G>T	c.(1669-1671)ccG>ccT	p.P557P	SFMBT2_ENST00000397167.1_Silent_p.P557P	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	557					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.P557P(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CGCATTTGCCCGGTCCCACCG	0.473																																																	1	Substitution - coding silent(1)	ovary(1)						C	,	0,4406		0,0,2203	114.0	108.0	110.0		1671,1671	-9.3	0.9	10		110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SFMBT2	NM_001018039.1,NM_001029880.2	,	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	,	557/895,557/895	7239537	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57713			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1671G>T	10.37:g.7239537C>A		Somatic		WXS	SOLID	Phase_I	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																				0.473	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1		NM_001029880	
SLC1A7	6512	hgsc.bcm.edu	37	1	53608000	53608000	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr1:53608000C>T	ENST00000371494.4	-	1	249	c.122G>A	c.(121-123)cGc>cAc	p.R41H	SLC1A7_ENST00000371491.4_Missense_Mutation_p.R41H	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	41			R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		TGGTGAGAGGCGCCGGGTCCT	0.647																																					NSCLC(128;80 1811 21245 38490 51715)												0													78.0	58.0	65.0					1																	53608000		2186	4276	6462	SO:0001583	missense	6512			U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"""Solute carriers"""	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.122G>A	1.37:g.53608000C>T	ENSP00000360549:p.Arg41His	Somatic		WXS	SOLID	Phase_I	Q5VVZ0|Q969Z8|Q9BW45	Missense_Mutation	SNP	ENST00000371494.4	37	CCDS574.1	.	.	.	.	.	.	.	.	.	.	T	6.090	0.384910	0.11524	.	.	ENSG00000162383	ENST00000371494;ENST00000371491	T;T	0.59083	0.29;0.29	5.53	-0.926	0.10455	.	0.287811	0.34906	N	0.003581	T	0.28167	0.0695	N	0.01874	-0.695	0.27780	N	0.943207	B;B	0.06786	0.001;0.0	B;B	0.08055	0.0;0.003	T	0.14727	-1.0462	10	0.37606	T	0.19	-19.0199	13.7256	0.62756	0.0:0.6784:0.0:0.3216	.	41;41	Q9BW45;O00341	.;EAA5_HUMAN	H	41	ENSP00000360549:R41H;ENSP00000360546:R41H	ENSP00000360546:R41H	R	-	2	0	SLC1A7	53380588	0.025000	0.19082	0.978000	0.43139	0.425000	0.31504	-0.248000	0.08854	-0.400000	0.07656	-2.410000	0.00221	CGC		0.647	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1		NM_006671	
SLC28A3	64078	hgsc.bcm.edu	37	9	86894964	86894964	+	Missense_Mutation	SNP	C	C	G	rs11568398	byFrequency	TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:86894964C>G	ENST00000376238.4	-	16	1803	c.1754G>C	c.(1753-1755)cGt>cCt	p.R585P	RP11-380F14.2_ENST00000419815.1_RNA|SLC28A3_ENST00000537648.1_Missense_Mutation_p.R516P	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	585			R -> H (in dbSNP:rs11568398). {ECO:0000269|PubMed:15738947}.		pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	GGCGATATCACGCTTTCTGGA	0.527																																					Ovarian(106;425 1539 34835 42413 43572)												0													70.0	54.0	60.0					9																	86894964		2203	4300	6503	SO:0001583	missense	64078			AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1754G>C	9.37:g.86894964C>G	ENSP00000365413:p.Arg585Pro	Somatic		WXS	SOLID	Phase_I	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	37	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.424007	0.25639	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	T;T	0.06371	3.31;3.31	6.03	-3.09	0.05331	Na dependent nucleoside transporter, C-terminal (1);	1.240630	0.05003	N	0.469367	T	0.04679	0.0127	N	0.11106	0.095	0.09310	N	1	B	0.10296	0.003	B	0.18561	0.022	T	0.44050	-0.9353	10	0.35671	T	0.21	1.854	13.7923	0.63148	0.0:0.3797:0.0:0.6203	.	585	Q9HAS3	S28A3_HUMAN	P	585;516	ENSP00000365413:R585P;ENSP00000446438:R516P	ENSP00000365413:R585P	R	-	2	0	SLC28A3	86084784	0.000000	0.05858	0.086000	0.20670	0.714000	0.41099	-1.301000	0.02749	-0.647000	0.05444	-1.038000	0.02383	CGT		0.527	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1		NM_022127	
SUFU	51684	hgsc.bcm.edu	37	10	104352445	104352445	+	Silent	SNP	C	C	A			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr10:104352445C>A	ENST00000369902.3	+	4	727	c.561C>A	c.(559-561)ccC>ccA	p.P187P	RNU6-43P_ENST00000384302.1_RNA|SUFU_ENST00000471000.1_3'UTR|SUFU_ENST00000423559.2_Silent_p.P187P|SUFU_ENST00000369899.2_Silent_p.P187P	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	187					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		AGATGCAGCCCGTGCAGACAC	0.577			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																														yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	0													121.0	103.0	109.0					10																	104352445		2203	4300	6503	SO:0001819	synonymous_variant	51684	Familial Cancer Database		AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.561C>A	10.37:g.104352445C>A		Somatic		WXS	SOLID	Phase_I	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Silent	SNP	ENST00000369902.3	37	CCDS7537.1																																																																																				0.577	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1		NM_016169	
TET2	54790	hgsc.bcm.edu;ucsc.edu	37	4	106196809	106196809	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr4:106196809T>G	ENST00000540549.1	+	11	6002	c.5142T>G	c.(5140-5142)aaT>aaG	p.N1714K	TET2_ENST00000380013.4_Missense_Mutation_p.N1714K|TET2_ENST00000513237.1_Missense_Mutation_p.N1735K|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1714					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTAGACCAAATGTACATCATG	0.423			"""Mis N, F"""		MDS																																			Rec	yes		4	4q24	54790	tet oncogene family member 2		L	0													122.0	102.0	108.0					4																	106196809		692	1591	2283	SO:0001583	missense	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5142T>G	4.37:g.106196809T>G	ENSP00000442788:p.Asn1714Lys	Somatic		WXS	SOLID	Phase_I	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	T	6.920	0.539387	0.13250	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02498	4.27;4.27;4.27	5.16	-1.56	0.08532	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.04634	0.0126	M	0.68317	2.08	0.09310	N	1	P;P	0.39717	0.684;0.491	B;B	0.41036	0.346;0.197	T	0.34850	-0.9812	9	0.27785	T	0.31	-2.9779	9.3639	0.38212	0.0:0.3678:0.0:0.6322	.	1735;1714	E7EQS8;Q6N021	.;TET2_HUMAN	K	1714;1735;1714	ENSP00000442788:N1714K;ENSP00000425443:N1735K;ENSP00000369351:N1714K	ENSP00000369351:N1714K	N	+	3	2	TET2	106416258	0.027000	0.19231	0.000000	0.03702	0.112000	0.19704	-0.198000	0.09505	-0.210000	0.10140	-0.456000	0.05471	AAT		0.423	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2		NM_017628	
TRIP11	9321	hgsc.bcm.edu	37	14	92436049	92436049	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr14:92436049C>T	ENST00000267622.4	-	21	6281	c.5908G>A	c.(5908-5910)Ggg>Agg	p.G1970R		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1970					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)		AGCACAACCCCAGCACTGTTG	0.438			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)			Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	0													73.0	77.0	76.0					14																	92436049		2203	4300	6503	SO:0001583	missense	9321			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.5908G>A	14.37:g.92436049C>T	ENSP00000267622:p.Gly1970Arg	Somatic		WXS	SOLID	Phase_I	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.33|17.33	3.362480|3.362480	0.61403|0.61403	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.20463|.	2.07|.	5.78|5.78	4.89|4.89	0.63831|0.63831	.|.	0.051564|.	0.85682|.	N|.	0.000000|.	T|.	0.73892|.	0.3645|.	M|M	0.74881|0.74881	2.28|2.28	0.54753|0.54753	D|D	0.999985|0.999985	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.986;0.999|.	T|.	0.74850|.	-0.3524|.	10|.	0.87932|.	D|.	0|.	.|.	14.7875|14.7875	0.69813|0.69813	0.0:0.9312:0.0:0.0688|0.0:0.9312:0.0:0.0688	.|.	1706;1970|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	R|X	1970;1706|1685	ENSP00000267622:G1970R|.	ENSP00000267622:G1970R|.	G|W	-|-	1|2	0|0	TRIP11|TRIP11	91505802|91505802	1.000000|1.000000	0.71417|0.71417	0.806000|0.806000	0.32338|0.32338	0.242000|0.242000	0.25591|0.25591	5.459000|5.459000	0.66685|0.66685	1.449000|1.449000	0.47699|0.47699	0.563000|0.563000	0.77884|0.77884	GGG|TGG		0.438	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			
TRPV5	56302	hgsc.bcm.edu;ucsc.edu	37	7	142609797	142609797	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr7:142609797A>G	ENST00000265310.1	-	13	1987	c.1639T>C	c.(1639-1641)Tac>Cac	p.Y547H		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	547					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TCCACGTCGTAGTTGGCAGGT	0.507																																																	0													214.0	178.0	190.0					7																	142609797		2203	4300	6503	SO:0001583	missense	56302			AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	3145	protein-coding gene	gene with protein product		606679	"""epithelial calcium channel 1"""	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1639T>C	7.37:g.142609797A>G	ENSP00000265310:p.Tyr547His	Somatic		WXS	SOLID	Phase_I	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.509049	0.27036	.	.	ENSG00000127412	ENST00000265310;ENST00000439304	T;T	0.75477	-0.94;-0.94	5.79	5.79	0.91817	Ion transport (1);	0.120824	0.56097	D	0.000022	D	0.82504	0.5051	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79381	-0.1827	10	0.24483	T	0.36	-9.3491	15.6042	0.76649	1.0:0.0:0.0:0.0	.	547	Q9NQA5	TRPV5_HUMAN	H	547;492	ENSP00000265310:Y547H;ENSP00000406361:Y492H	ENSP00000265310:Y547H	Y	-	1	0	TRPV5	142319919	1.000000	0.71417	0.993000	0.49108	0.159000	0.22180	5.699000	0.68310	2.338000	0.79540	0.533000	0.62120	TAC		0.507	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1		NM_019841	
UMODL1	89766	hgsc.bcm.edu;ucsc.edu	37	21	43547853	43547853	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr21:43547853G>C	ENST00000408910.2	+	20	3602	c.3602G>C	c.(3601-3603)aGg>aCg	p.R1201T	UMODL1_ENST00000400427.1_Missense_Mutation_p.R1257T|UMODL1_ENST00000408989.2_Missense_Mutation_p.R1329T|UMODL1_ENST00000400424.2_Missense_Mutation_p.R1129T|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1201	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TTCAAGCTGAGGATCTTTTCC	0.507																																					Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)												0													124.0	122.0	123.0					21																	43547853		2017	4182	6199	SO:0001583	missense	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3602G>C	21.37:g.43547853G>C	ENSP00000386147:p.Arg1201Thr	Somatic		WXS	SOLID	Phase_I	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	7.040	0.562261	0.13498	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	3.67	0.14	0.14804	Zona pellucida sperm-binding protein (3);	0.287943	0.23608	N	0.046368	T	0.75679	0.3882	L	0.53249	1.67	0.23762	N	0.996917	P;B	0.36535	0.557;0.279	B;B	0.39258	0.295;0.194	T	0.64118	-0.6482	9	.	.	.	-14.6857	6.4564	0.21932	0.5867:0.0:0.4133:0.0	.	1329;1201	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	1257;1129;1329;1201;86	ENSP00000383279:R1257T;ENSP00000383276:R1129T;ENSP00000386126:R1329T;ENSP00000386147:R1201T	.	R	+	2	0	UMODL1	42420922	1.000000	0.71417	0.640000	0.29408	0.019000	0.09904	1.945000	0.40273	0.015000	0.14971	-0.367000	0.07326	AGG		0.507	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			
USP18	11274	hgsc.bcm.edu	37	22	18640565	18640565	+	Silent	SNP	C	C	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr22:18640565C>T	ENST00000215794.7	+	2	565	c.135C>T	c.(133-135)ccC>ccT	p.P45P		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	45					cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GAGAGCGTCCCAGGGCCTGGG	0.562																																																	0													105.0	104.0	104.0					22																	18640565		2203	4300	6503	SO:0001819	synonymous_variant	11274			AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"""Ubiquitin-specific peptidases"""	12616	protein-coding gene	gene with protein product		607057	"""ubiquitin specific protease 18"""			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.135C>T	22.37:g.18640565C>T		Somatic		WXS	SOLID	Phase_I	Q53Y90|Q6IAD9|Q9NY71	Silent	SNP	ENST00000215794.7	37	CCDS13752.1																																																																																				0.562	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1			
USP9X	8239	hgsc.bcm.edu	37	X	41047253	41047253	+	Silent	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chrX:41047253A>G	ENST00000324545.8	+	25	4326	c.3693A>G	c.(3691-3693)agA>agG	p.R1231R	USP9X_ENST00000378308.2_Silent_p.R1231R	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1231					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.R1224S(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						AGGCTTCAAGATATATGCCTG	0.323																																					Ovarian(172;1807 2695 35459 49286)												1	Substitution - Missense(1)	breast(1)											67.0	60.0	62.0					X																	41047253		2178	4283	6461	SO:0001819	synonymous_variant	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3693A>G	X.37:g.41047253A>G		Somatic		WXS	SOLID	Phase_I	O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	37	CCDS43930.1																																																																																				0.323	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4		NM_004652	
VCP	7415	hgsc.bcm.edu;ucsc.edu	37	9	35062023	35062023	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr9:35062023A>T	ENST00000358901.6	-	9	1953	c.1058T>A	c.(1057-1059)aTt>aAt	p.I353N		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	353					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AGCTGGGTCAATGCTGTTGGG	0.502																																																	0													271.0	192.0	218.0					9																	35062023		2203	4300	6503	SO:0001583	missense	7415			AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1058T>A	9.37:g.35062023A>T	ENSP00000351777:p.Ile353Asn	Somatic		WXS	SOLID	Phase_I	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	37	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.489989	0.84962	.	.	ENSG00000165280	ENST00000358901	D	0.94758	-3.51	6.17	6.17	0.99709	ATPase, AAA-type, conserved site (1);ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.98264	0.9425	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99433	1.0936	10	0.87932	D	0	-41.7106	16.8222	0.85835	1.0:0.0:0.0:0.0	.	353	P55072	TERA_HUMAN	N	353	ENSP00000351777:I353N	ENSP00000351777:I353N	I	-	2	0	VCP	35052023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	ATT		0.502	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1		NM_007126	
ZBTB38	253461	hgsc.bcm.edu	37	3	141164552	141164552	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4160-01A-02D-1366-10	TCGA-BP-4160-11A-01D-1806-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91fc0b5e-0cb8-48f8-94c0-abf7e668e965	5a1faf3e-afc7-4b3e-880d-5a767db34ab5	g.chr3:141164552A>G	ENST00000514251.1	+	4	3601	c.3322A>G	c.(3322-3324)Acc>Gcc	p.T1108A	ZBTB38_ENST00000321464.5_Missense_Mutation_p.T1109A|ZBTB38_ENST00000441582.2_Missense_Mutation_p.T1108A					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						GTATCTCTCCACCAAAAGGAA	0.458																																																	0													88.0	83.0	85.0					3																	141164552		1907	4133	6040	SO:0001583	missense	253461			BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.3322A>G	3.37:g.141164552A>G	ENSP00000426387:p.Thr1108Ala	Somatic		WXS	SOLID	Phase_I		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.579071	0.65878	.	.	ENSG00000177311	ENST00000514251;ENST00000441582;ENST00000321464	T;T;T	0.08984	3.03;3.03;3.04	5.81	5.81	0.92471	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.16214	0.0390	N	0.21508	0.67	0.36567	D	0.872759	D;D	0.76494	0.999;0.999	D;D	0.68039	0.955;0.955	T	0.22417	-1.0217	9	.	.	.	-27.2877	16.1699	0.81801	1.0:0.0:0.0:0.0	.	1109;1108	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	A	1108;1108;1109	ENSP00000426387:T1108A;ENSP00000406955:T1108A;ENSP00000372635:T1109A	.	T	+	1	0	ZBTB38	142647242	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.164000	0.71885	2.217000	0.71921	0.533000	0.62120	ACC		0.458	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			
