#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
ACTN2	88	broad.mit.edu;ucsc.edu	37	1	236911030	236911030	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:236911030G>T	ENST00000366578.4	+	13	1636	c.1470G>T	c.(1468-1470)tgG>tgT	p.W490C	ACTN2_ENST00000546208.1_5'UTR|ACTN2_ENST00000542672.1_Missense_Mutation_p.W490C	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	490					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GTGACCAGTGGGACCGACTGG	0.398																																																	0													48.0	51.0	50.0					1																	236911030		2203	4300	6503	SO:0001583	missense	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1470G>T	1.37:g.236911030G>T	ENSP00000355537:p.Trp490Cys	Somatic		WXS	Illumina GAIIx	Phase_I	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.819893	0.90873	.	.	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000545611	T;T	0.68903	-0.36;-0.36	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.87830	0.6276	H	0.94847	3.59	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	0.995;1.0;1.0;0.998	D	0.90184	0.4245	10	0.87932	D	0	.	20.2699	0.98469	0.0:0.0:1.0:0.0	.	275;490;260;490	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	C	490;490;259	ENSP00000443495:W490C;ENSP00000355537:W490C	ENSP00000355537:W490C	W	+	3	0	ACTN2	234977653	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.760000	0.98935	2.854000	0.98071	0.655000	0.94253	TGG		0.398	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1		NM_001103	
IGHV1-8	28472	broad.mit.edu	37	14	106539313	106539313	+	RNA	SNP	G	G	A	rs201374326	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:106539313G>A	ENST00000390599.2	-	0	178									immunoglobulin heavy variable 1-8																		CCTTGCAGGAGACCTTCACTG	0.547																																																	0													105.0	78.0	87.0					14																	106539313		1816	3497	5313			8755			M99637		14q32.33	2012-02-08			ENSG00000211939			"""Immunoglobulins / IGH locus"""	5559	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152284		14.37:g.106539313G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000390599.2	37																																																																																					0.547	IGHV1-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325672.1		NG_001019	
IGHV1-8	28472	broad.mit.edu	37	14	106539361	106539361	+	RNA	SNP	C	C	A	rs587598643	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:106539361C>A	ENST00000390599.2	-	0	130									immunoglobulin heavy variable 1-8																		CAGACTGCACCAGCTGCACCT	0.532													.|||	203	0.0405351	0.0061	0.0432	5008	,	,		7713	0.0188		0.0666	False		,,,				2504	0.0808																0													80.0	63.0	69.0					14																	106539361		1782	3397	5179			8755			M99637		14q32.33	2012-02-08			ENSG00000211939			"""Immunoglobulins / IGH locus"""	5559	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152284		14.37:g.106539361C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000390599.2	37																																																																																					0.532	IGHV1-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325672.1		NG_001019	
IGHV1-8	28472	broad.mit.edu	37	14	106539367	106539367	+	RNA	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:106539367C>G	ENST00000390599.2	-	0	124									immunoglobulin heavy variable 1-8																		GCACCAGCTGCACCTGGGAGT	0.527																																																	0													78.0	61.0	67.0					14																	106539367		1785	3395	5180			8755			M99637		14q32.33	2012-02-08			ENSG00000211939			"""Immunoglobulins / IGH locus"""	5559	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152284		14.37:g.106539367C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000390599.2	37																																																																																					0.527	IGHV1-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325672.1		NG_001019	
Unknown	0	broad.mit.edu	37	14	106919168	106919168	+	IGR	DEL	C	C	-	rs139643696	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:106919168delC								IGHV4-39 (41042 upstream) : IGHV3-43 (7019 downstream)																							ACGTTAACCTCCCCCTCACTG	0.557													CCCC|CCCCC|CCCC|insertion	1476	0.294728	0.4289	0.2233	5008	,	,		15151	0.1548		0.2644	False		,,,				2504	0.3395																0																																										SO:0001628	intergenic_variant	8755																															14.37:g.106919168delC		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.557									
ADCY7	113	hgsc.bcm.edu	37	16	50340985	50340986	+	Frame_Shift_Ins	INS	-	-	C	rs74793314		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:50340985_50340986insC	ENST00000394697.2	+	15	2117_2118	c.1777_1778insC	c.(1777-1779)gccfs	p.A593fs	ADCY7_ENST00000537579.1_3'UTR|ADCY7_ENST00000538642.1_Frame_Shift_Ins_p.A593fs|ADCY7_ENST00000254235.3_Frame_Shift_Ins_p.A593fs|ADCY7_ENST00000566433.2_Frame_Shift_Ins_p.A593fs			P51828	ADCY7_HUMAN	adenylate cyclase 7	593					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		CATCCCCCGGGCCCGCCACGAC	0.658																																																	0																																										SO:0001589	frameshift_variant	113			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.1780dupC	16.37:g.50340988_50340988dupC	ENSP00000378187:p.Ala593fs	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVA6	Frame_Shift_Ins	INS	ENST00000394697.2	37	CCDS10741.1																																																																																				0.658	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			
AHNAK2	113146	hgsc.bcm.edu	37	14	105412138	105412138	+	Missense_Mutation	SNP	A	A	G	rs200384326		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:105412138A>G	ENST00000333244.5	-	7	9769	c.9650T>C	c.(9649-9651)cTc>cCc	p.L3217P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3217						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			AGCTCCCTCGAGAACGTGGCC	0.602																																																	0													112.0	72.0	85.0					14																	105412138		1914	4004	5918	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9650T>C	14.37:g.105412138A>G	ENSP00000353114:p.Leu3217Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	2.736	-0.263306	0.05754	.	.	ENSG00000185567	ENST00000333244	T	0.00554	6.64	2.59	2.59	0.31030	.	.	.	.	.	T	0.00178	0.0005	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17837	-1.0356	8	0.30078	T	0.28	.	5.3502	0.16032	0.1716:0.0:0.8284:0.0	.	3217	Q8IVF2	AHNK2_HUMAN	P	3217	ENSP00000353114:L3217P	ENSP00000353114:L3217P	L	-	2	0	AHNAK2	104483183	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.587000	0.05780	0.297000	0.22615	-0.971000	0.02607	CTC		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412554	105412554	+	Silent	SNP	T	T	G	rs12436986	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:105412554T>G	ENST00000333244.5	-	7	9353	c.9234A>C	c.(9232-9234)ggA>ggC	p.G3078G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3078						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTATCTGGGGTCCCTTGCGAT	0.627													.|||	2579	0.514976	0.5688	0.4683	5008	,	,		13838	0.3938		0.494	False		,,,				2504	0.6217																0								G		1294,2350		564,166,1092	67.0	77.0	74.0		9234	-1.0	0.0	14	dbSNP_120	74	2121,5993		930,261,2866	no	coding-synonymous	AHNAK2	NM_138420.2		1494,427,3958	GG,GT,TT		26.14,35.5104,29.0441		3078/5796	105412554	3415,8343	1822	4057	5879	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9234A>C	14.37:g.105412554T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
AHNAK2	113146	hgsc.bcm.edu	37	14	105419047	105419047	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:105419047A>C	ENST00000333244.5	-	7	2860	c.2741T>G	c.(2740-2742)gTg>gGg	p.V914G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	914						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGGCAGGTGCACTTTGGGGCC	0.612																																																	0													142.0	164.0	157.0					14																	105419047		1846	4091	5937	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2741T>G	14.37:g.105419047A>C	ENSP00000353114:p.Val914Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	2.080	-0.411011	0.04799	.	.	ENSG00000185567	ENST00000333244	T	0.01871	4.59	3.89	2.98	0.34508	.	.	.	.	.	T	0.00524	0.0017	N	0.00021	-2.75	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46345	-0.9198	9	0.20519	T	0.43	-4.1188	8.1603	0.31194	0.1795:0.6471:0.1734:0.0	.	914	Q8IVF2	AHNK2_HUMAN	G	914	ENSP00000353114:V914G	ENSP00000353114:V914G	V	-	2	0	AHNAK2	104490092	0.813000	0.29090	0.004000	0.12327	0.003000	0.03518	1.857000	0.39399	0.152000	0.19188	-0.323000	0.08544	GTG		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496323	39496325	+	In_Frame_Del	DEL	AAC	AAC	-	rs140936762|rs139292|rs201177427	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr22:39496323_39496325delAAC	ENST00000401756.1	+	2	116_118	c.40_42delAAC	c.(40-42)aacdel	p.N15del	APOBEC3H_ENST00000421988.2_In_Frame_Del_p.N15del|APOBEC3H_ENST00000348946.4_In_Frame_Del_p.N15del|APOBEC3H_ENST00000442487.3_In_Frame_Del_p.N15del	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	15			Missing (decreases protein stability). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CTTACAGTTTAACAACAAGCGCC	0.532														1590	0.317492	0.3071	0.2795	5008	,	,		17995	0.2579		0.339	False		,,,				2504	0.3978																0									,,,	1382,2882		240,902,990					,,,	-1.8	0.2		dbSNP_129	82	2684,5570		426,1832,1869	no	coding,coding,coding,coding	APOBEC3H	NM_181773.3,NM_001166004.1,NM_001166003.1,NM_001166002.1	,,,	666,2734,2859	A1A1,A1R,RR		32.5176,32.4109,32.4812	,,,	,,,		4066,8452				SO:0001651	inframe_deletion	164668			BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.40_42delAAC	22.37:g.39496326_39496328delAAC	ENSP00000385741:p.Asn15del	Somatic		WXS	Illumina HiSeq	Phase_I	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	In_Frame_Del	DEL	ENST00000401756.1	37	CCDS54530.1																																																																																				0.532	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1		NM_181773	
AQP7	364	hgsc.bcm.edu	37	9	33385784	33385784	+	Missense_Mutation	SNP	C	C	G	rs114937176		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:33385784C>G	ENST00000537089.1	-	6	648	c.330G>C	c.(328-330)gaG>gaC	p.E110D	AQP7_ENST00000377425.4_Missense_Mutation_p.E145D|AQP7_ENST00000541274.1_Missense_Mutation_p.G71R|AQP7_ENST00000539936.1_Missense_Mutation_p.E202D			O14520	AQP7_HUMAN	aquaporin 7	202					excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TCACCAGCGCCTCTGTTCCTG	0.617																																																	0													112.0	101.0	105.0					9																	33385784		2203	4300	6503	SO:0001583	missense	364			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.330G>C	9.37:g.33385784C>G	ENSP00000441619:p.Glu110Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	11.02|11.02	1.516950|1.516950	0.27123|0.27123	.|.	.|.	ENSG00000165269|ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503|ENST00000541274	D;D;D;D;D;D;D;D;D|T	0.85258|0.59083	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96|0.29	5.02|5.02	0.853|0.853	0.19001|0.19001	Aquaporin-like (2);|.	0.285780|.	0.38326|.	N|.	0.001735|.	T|T	0.34600|0.34600	0.0903|0.0903	N|N	0.25201|0.25201	0.72|0.72	0.35300|0.35300	P|P	0.21709|0.21709	B;B;B;B|B	0.23377|0.30406	0.044;0.005;0.084;0.084|0.278	B;B;B;B|B	0.34779|0.24155	0.107;0.063;0.189;0.189|0.051	T|T	0.38045|0.38045	-0.9679|-0.9679	9|8	0.62326|0.87932	D|D	0.03|0	-2.4877|-2.4877	1.0491|1.0491	0.01576|0.01576	0.3087:0.3628:0.1501:0.1784|0.3087:0.3628:0.1501:0.1784	.|.	201;202;145;202|71	Q5T5M0;B7Z4U2;Q6P5T0;O14520|B7Z7F6	.;.;.;AQP7_HUMAN|.	D|R	110;201;70;202;145;110;201;202;138|71	ENSP00000441619:E110D;ENSP00000368821:E201D;ENSP00000412868:E70D;ENSP00000297988:E202D;ENSP00000396111:E145D;ENSP00000410138:E110D;ENSP00000368820:E201D;ENSP00000439534:E202D;ENSP00000368817:E138D|ENSP00000438860:G71R	ENSP00000297988:E202D|ENSP00000438860:G71R	E|G	-|-	3|1	2|0	AQP7|AQP7	33375784|33375784	0.949000|0.949000	0.32298|0.32298	0.992000|0.992000	0.48379|0.48379	0.191000|0.191000	0.23601|0.23601	0.131000|0.131000	0.15870|0.15870	0.663000|0.663000	0.31027|0.31027	0.645000|0.645000	0.84053|0.84053	GAG|GGC		0.617	AQP7-202	KNOWN	basic	protein_coding	protein_coding			NM_001170	
AQP7	364	hgsc.bcm.edu	37	9	33385815	33385815	+	Missense_Mutation	SNP	T	T	C	rs62542745		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:33385815T>C	ENST00000537089.1	-	6	617	c.299A>G	c.(298-300)cAg>cGg	p.Q100R	AQP7_ENST00000377425.4_Missense_Mutation_p.Q135R|AQP7_ENST00000541274.1_Silent_p.P60P|AQP7_ENST00000539936.1_Missense_Mutation_p.Q192R			O14520	AQP7_HUMAN	aquaporin 7	192					excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		GTTGTTCTCCTGGTCCGTGAT	0.612																																																	0													123.0	107.0	113.0					9																	33385815		2203	4300	6503	SO:0001583	missense	364			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.299A>G	9.37:g.33385815T>C	ENSP00000441619:p.Gln100Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.	.	.	.	.	.	.	.	.	.	t	2.177	-0.388519	0.04932	.	.	ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503	D;D;D;D;D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93	5.02	3.85	0.44370	Aquaporin-like (2);	0.260173	0.44483	D	0.000447	T	0.69360	0.3102	N	0.20483	0.58	0.09310	N	1	B;B;B;B	0.14012	0.001;0.001;0.001;0.009	B;B;B;B	0.17098	0.006;0.006;0.01;0.017	T	0.51260	-0.8728	10	0.13853	T	0.58	-14.4887	4.9508	0.14013	0.0:0.0932:0.1892:0.7176	rs62542745	191;192;135;192	Q5T5M0;B7Z4U2;Q6P5T0;O14520	.;.;.;AQP7_HUMAN	R	100;191;60;192;135;100;191;192;128	ENSP00000441619:Q100R;ENSP00000368821:Q191R;ENSP00000412868:Q60R;ENSP00000297988:Q192R;ENSP00000396111:Q135R;ENSP00000410138:Q100R;ENSP00000368820:Q191R;ENSP00000439534:Q192R;ENSP00000368817:Q128R	ENSP00000297988:Q192R	Q	-	2	0	AQP7	33375815	0.007000	0.16637	0.339000	0.25562	0.162000	0.22319	0.341000	0.19909	0.903000	0.36546	0.524000	0.50904	CAG		0.612	AQP7-202	KNOWN	basic	protein_coding	protein_coding			NM_001170	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12847385	12847385	+	Splice_Site	SNP	G	G	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:12847385G>T	ENST00000379672.5	+	10	1033		c.e10-1		ARHGAP44_ENST00000262444.9_Splice_Site|ARHGAP44_ENST00000340825.3_Splice_Site	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44						exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CCTCCCCTCAGAGGCCTGGGT	0.557																																																	0													23.0	28.0	26.0					17																	12847385		1961	4165	6126	SO:0001630	splice_region_variant	9912				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.734-1G>T	17.37:g.12847385G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Splice_Site	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.565824	0.86439	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4003	0.87458	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP44	12788110	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	9.813000	0.99286	2.781000	0.95711	0.655000	0.94253	.		0.557	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1		NM_014859	Intron
ARHGEF1	9138	broad.mit.edu;hgsc.bcm.edu	37	19	42408211	42408211	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:42408211T>G	ENST00000354532.3	+	21	2090	c.1942T>G	c.(1942-1944)Ttg>Gtg	p.L648V	ARHGEF1_ENST00000599846.1_Missense_Mutation_p.L704V|ARHGEF1_ENST00000347545.4_Missense_Mutation_p.L615V|ARHGEF1_ENST00000337665.4_Missense_Mutation_p.L663V|ARHGEF1_ENST00000378152.4_Missense_Mutation_p.L630V	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	648	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		CAAGAAGAAATTGGTCCACGA	0.622																																																	0													118.0	119.0	118.0					19																	42408211		2203	4300	6503	SO:0001583	missense	9138			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.1942T>G	19.37:g.42408211T>G	ENSP00000346532:p.Leu648Val	Somatic		WXS	Illumina HiSeq	Phase_I	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Missense_Mutation	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.038121	0.54896	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000337665;ENST00000378152	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	4.08	-4.07	0.03975	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.077244	0.49916	D	0.000129	T	0.78444	0.4284	M	0.80847	2.515	0.45502	D	0.998463	B;B;P;B	0.36392	0.149;0.441;0.551;0.352	B;B;B;B	0.43508	0.083;0.307;0.345;0.422	T	0.75991	-0.3122	10	0.72032	D	0.01	-9.6409	12.2805	0.54760	0.0:0.6431:0.0:0.3569	.	630;663;615;648	Q6NX52;Q92888-3;Q92888-2;Q92888	.;.;.;ARHG1_HUMAN	V	648;615;663;630	ENSP00000346532:L648V;ENSP00000344429:L615V;ENSP00000337261:L663V;ENSP00000367394:L630V	ENSP00000337261:L663V	L	+	1	2	ARHGEF1	47100051	0.000000	0.05858	0.906000	0.35671	0.985000	0.73830	-0.971000	0.03806	-0.818000	0.04329	0.456000	0.33151	TTG		0.622	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1		NM_199002	
ARMC10	83787	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	102716238	102716238	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:102716238G>T	ENST00000323716.3	+	2	546	c.154G>T	c.(154-156)Ggg>Tgg	p.G52W	ARMC10_ENST00000425331.1_Intron|FBXL13_ENST00000379308.3_5'Flank|FBXL13_ENST00000379305.3_5'Flank|FBXL13_ENST00000313221.4_5'Flank|FBXL13_ENST00000455112.2_5'Flank|ARMC10_ENST00000428183.2_Missense_Mutation_p.G52W|FBXL13_ENST00000393772.2_5'Flank|ARMC10_ENST00000441711.2_Intron|ARMC10_ENST00000454559.1_Intron|FBXL13_ENST00000456695.1_5'Flank|ARMC10_ENST00000541300.1_Intron|FBXL13_ENST00000379306.3_5'Flank|FBXL13_ENST00000471074.1_5'Flank	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	52					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						CCTGGAAGAAGGGACGTCAGA	0.602																																																	0													50.0	48.0	49.0					7																	102716238		2203	4300	6503	SO:0001583	missense	83787			AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"""Armadillo repeat containing"""	21706	protein-coding gene	gene with protein product	"""specific Splicing Variant involved in Hepatocarcinogenesis"""	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.154G>T	7.37:g.102716238G>T	ENSP00000319412:p.Gly52Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	37	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.762288	0.49468	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000434153	T;T	0.47177	0.89;0.85	2.97	-2.15	0.07102	.	1.523220	0.05183	U	0.501709	T	0.38161	0.1030	L	0.51422	1.61	0.09310	N	0.999998	B;B	0.14805	0.011;0.001	B;B	0.12837	0.008;0.001	T	0.35001	-0.9806	10	0.66056	D	0.02	5.7206	2.5104	0.04655	0.3327:0.0:0.2999:0.3674	.	52;52	Q8N2F6-3;Q8N2F6	.;ARM10_HUMAN	W	52	ENSP00000319412:G52W;ENSP00000398201:G52W	ENSP00000319412:G52W	G	+	1	0	ARMC10	102503474	0.000000	0.05858	0.000000	0.03702	0.275000	0.26752	-0.566000	0.05922	-0.552000	0.06167	0.591000	0.81541	GGG		0.602	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1		NM_031905	
ASCC3	10973	broad.mit.edu	37	6	100966004	100966005	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:100966004_100966005delCA	ENST00000369162.2	-	38	6133_6134	c.5789_5790delTG	c.(5788-5790)gtgfs	p.V1930fs		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1930	SEC63 2.		V -> M (in dbSNP:rs3213542).		cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GGTTTGCAGCCACGTCCAGCAT	0.465																																																	0																																										SO:0001589	frameshift_variant	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.5789_5790delTG	6.37:g.100966004_100966005delCA	ENSP00000358159:p.Val1930fs	Somatic		WXS	Illumina GAIIx	Phase_I	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	37	CCDS5046.1																																																																																				0.465	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2		NM_006828	
ATF1	466	broad.mit.edu	37	12	51213515	51213515	+	Frame_Shift_Del	DEL	G	G	-	rs565435031		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:51213515delG	ENST00000262053.3	+	7	791	c.769delG	c.(769-771)gaafs	p.E258fs	ATF1_ENST00000539132.1_Frame_Shift_Del_p.E123fs	NM_005171.4	NP_005162.1	P18846	ATF1_HUMAN	activating transcription factor 1	258	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular protein complex assembly (GO:0043623)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to cobalt ion (GO:0032025)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/ATF1(347)|FUS/ATF1(4)	breast(1)|large_intestine(1)|ovary(2)	4					Pseudoephedrine(DB00852)	AACTCTAATAGAAGAGTTAAA	0.318			T	"""EWSR1, FUS"""	"""malignant melanoma of soft parts , angiomatoid fibrous histiocytoma """																																			Dom	yes		12	12q13	466	activating transcription factor 1		"""E, M"""	0													32.0	35.0	34.0					12																	51213515		2203	4295	6498	SO:0001589	frameshift_variant	466			BC029619	CCDS8803.1	12q13	2014-05-13			ENSG00000123268	ENSG00000123268		"""basic leucine zipper proteins"""	783	protein-coding gene	gene with protein product		123803				8401579	Standard	NM_005171		Approved	TREB36	uc001rww.4	P18846		ENST00000262053.3:c.769delG	12.37:g.51213515delG	ENSP00000262053:p.Glu258fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4DRF9|P25168|Q9H4A8	Frame_Shift_Del	DEL	ENST00000262053.3	37	CCDS8803.1																																																																																				0.318	ATF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404285.1		NM_005171	
AVL9	23080	broad.mit.edu	37	7	32615623	32615623	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:32615623A>G	ENST00000318709.4	+	13	1848	c.1627A>G	c.(1627-1629)Act>Gct	p.T543A	AVL9_ENST00000409301.1_Missense_Mutation_p.T543A|AVL9_ENST00000404479.1_Intron	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	543					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ATGGAAGAATACTCACAACTA	0.403																																																	0													168.0	158.0	162.0					7																	32615623		2203	4300	6503	SO:0001583	missense	23080			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1627A>G	7.37:g.32615623A>G	ENSP00000315568:p.Thr543Ala	Somatic		WXS	Illumina GAIIx	Phase_I	Q92573	Missense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.884872	0.91814	.	.	ENSG00000105778	ENST00000318709;ENST00000409301	T;T	0.70399	-0.48;-0.35	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.84611	0.5510	M	0.81497	2.545	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	D	0.86851	0.2023	10	0.87932	D	0	-22.1025	16.0234	0.80516	1.0:0.0:0.0:0.0	.	543	Q8NBF6	AVL9_HUMAN	A	543	ENSP00000315568:T543A;ENSP00000387011:T543A	ENSP00000315568:T543A	T	+	1	0	AVL9	32582148	1.000000	0.71417	0.954000	0.39281	0.986000	0.74619	7.092000	0.76930	2.172000	0.68678	0.533000	0.62120	ACT		0.403	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1		NM_015060	
BAHCC1	57597	hgsc.bcm.edu	37	17	79424537	79424537	+	Silent	SNP	C	C	T	rs34224936	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:79424537C>T	ENST00000307745.7	+	21	4960	c.4960C>T	c.(4960-4962)Ctg>Ttg	p.L1654L																								TGTGGCCGTGCTGGGGCCCTC	0.632													C|||	1526	0.304712	0.2821	0.4222	5008	,	,		13963	0.1438		0.3807	False		,,,				2504	0.3395																0								C		1245,2881		195,855,1013	17.0	24.0	21.0		4789	3.9	1.0	17	dbSNP_126	21	3100,5308		559,1982,1663	no	coding-synonymous	BAHCC1	NM_001080519.2		754,2837,2676	TT,TC,CC		36.8696,30.1745,34.6657		1597/2552	79424537	4345,8189	2063	4204	6267	SO:0001819	synonymous_variant	57597																														ENST00000307745.7:c.4960C>T	17.37:g.79424537C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000307745.7	37																																																																																					0.632	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				
BCAN	63827	broad.mit.edu;hgsc.bcm.edu	37	1	156622274	156622274	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:156622274C>G	ENST00000329117.5	+	8	1868	c.1532C>G	c.(1531-1533)gCa>gGa	p.A511G	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.A511G	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	511					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGGCGCCAGCAAGGGCAGTC	0.652																																																	0													17.0	16.0	17.0					1																	156622274		2202	4298	6500	SO:0001583	missense	63827			BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1532C>G	1.37:g.156622274C>G	ENSP00000331210:p.Ala511Gly	Somatic		WXS	Illumina HiSeq	Phase_I	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	1.559	-0.537211	0.04082	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.15718	2.4;3.0	4.37	3.39	0.38822	.	0.602886	0.14076	N	0.343027	T	0.03390	0.0098	L	0.29908	0.895	0.09310	N	1	P;B	0.40250	0.709;0.075	B;B	0.34093	0.175;0.027	T	0.34925	-0.9809	10	0.25106	T	0.35	-4.9531	7.6999	0.28617	0.0:0.8755:0.0:0.1245	.	511;511	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	G	450;511;511	ENSP00000331210:A511G;ENSP00000354925:A511G	ENSP00000255029:A450G	A	+	2	0	BCAN	154888898	0.001000	0.12720	0.026000	0.17262	0.029000	0.11900	0.847000	0.27696	0.946000	0.37632	0.455000	0.32223	GCA		0.652	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2		NM_021948	
BRCA1	672	broad.mit.edu;ucsc.edu	37	17	41234582	41234582	+	Missense_Mutation	SNP	G	G	C	rs80357649		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:41234582G>C	ENST00000357654.3	-	12	4314	c.4196C>G	c.(4195-4197)aCc>aGc	p.T1399S	BRCA1_ENST00000351666.3_Missense_Mutation_p.T216S|BRCA1_ENST00000468300.1_Missense_Mutation_p.T296S|BRCA1_ENST00000352993.3_Missense_Mutation_p.T257S|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.T1103S|BRCA1_ENST00000493795.1_Missense_Mutation_p.T1352S|BRCA1_ENST00000491747.2_Missense_Mutation_p.T296S|BRCA1_ENST00000346315.3_Missense_Mutation_p.T1399S|BRCA1_ENST00000354071.3_Missense_Mutation_p.T1399S|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.T1399S	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1399	Interaction with PALB2.				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)			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)		ATGTTGCATGGTATCCCTCTG	0.383			"""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	0			GRCh37	CD032728	BRCA1	D	rs80357649						113.0	98.0	103.0					17																	41234582		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.4196C>G	17.37:g.41234582G>C	ENSP00000350283:p.Thr1399Ser	Somatic		WXS	Illumina GAIIx	Phase_I	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.67|17.67	3.446423|3.446423	0.63178|0.63178	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000461574|ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919;ENST00000487825	.|D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.90955	.|-2.37;-2.47;-2.45;-2.46;-2.44;-2.27;-2.29;-2.76;-2.37;-2.49;-2.16;-1.92;-2.35;-1.81	5.35|5.35	4.39|4.39	0.52855|0.52855	.|.	.|0.228468	.|0.31167	.|N	.|0.008139	D|D	0.91673|0.91673	0.7368|0.7368	L|L	0.32530|0.32530	0.975|0.975	0.25262|0.25262	N|N	0.989586|0.989586	.|D;D;P;D;P;P;B;P	.|0.69078	.|0.966;0.996;0.91;0.997;0.91;0.91;0.255;0.946	.|P;D;B;D;B;B;B;P	.|0.73708	.|0.505;0.968;0.388;0.981;0.388;0.388;0.053;0.592	D|D	0.85526|0.85526	0.1206|0.1206	5|10	.|0.87932	.|D	.|0	.|.	12.3453|12.3453	0.55118|0.55118	0.0774:0.0:0.9226:0.0|0.0774:0.0:0.9226:0.0	.|.	.|295;249;295;296;296;1399;1399;1399	.|E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.|.;.;.;.;.;.;BRCA1_HUMAN;.	A|S	164|1399;1399;1399;257;1399;216;1103;296;249;1399;1352;295;295;170;249;171	.|ENSP00000350283:T1399S;ENSP00000326002:T1399S;ENSP00000312236:T257S;ENSP00000246907:T1399S;ENSP00000338007:T216S;ENSP00000310938:T1103S;ENSP00000417148:T296S;ENSP00000377294:T249S;ENSP00000418960:T1399S;ENSP00000418775:T1352S;ENSP00000420412:T295S;ENSP00000419481:T170S;ENSP00000418819:T249S;ENSP00000418212:T171S	.|ENSP00000310938:T1103S	P|T	-|-	1|2	0|0	BRCA1|BRCA1	38488108|38488108	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.980000|0.980000	0.70556|0.70556	2.002000|2.002000	0.40835|0.40835	1.495000|1.495000	0.48549|0.48549	0.555000|0.555000	0.69702|0.69702	CCA|ACC		0.383	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2		NM_007294	
IRF2BPL	64207	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	77491962	77491962	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr14:77491962G>A	ENST00000238647.3	-	1	3072	c.2174C>T	c.(2173-2175)aCg>aTg	p.T725M		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	725					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						AACGAAATGCGTATCCTCCAA	0.582																																																	0													64.0	53.0	57.0					14																	77491962		2203	4300	6503	SO:0001583	missense	0			AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2174C>T	14.37:g.77491962G>A	ENSP00000238647:p.Thr725Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	37	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.824684	0.71143	.	.	ENSG00000119669	ENST00000238647	T	0.78246	-1.16	4.64	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	U	0.000000	D	0.88727	0.6515	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90587	0.4534	10	0.87932	D	0	.	16.6461	0.85177	0.0:0.0:1.0:0.0	.	725	Q9H1B7	I2BPL_HUMAN	M	725	ENSP00000238647:T725M	ENSP00000238647:T725M	T	-	2	0	IRF2BPL	76561715	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.611000	0.98342	2.407000	0.81776	0.462000	0.41574	ACG		0.582	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1		NM_024496	
C19orf33	64073	hgsc.bcm.edu	37	19	38795587	38795587	+	Missense_Mutation	SNP	A	A	G	rs76762399		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:38795587A>G	ENST00000301246.5	+	4	405	c.304A>G	c.(304-306)Aag>Gag	p.K102E	C19orf33_ENST00000588605.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	102						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			gggcaagaagaaggagGCTCC	0.602																																																	0													80.0	84.0	82.0					19																	38795587		2198	4298	6496	SO:0001583	missense	64073			AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"""immortalization-upregulated protein"", ""HAI-2 related small protein"", ""hepatocyte growth factor activator inhibitor type 2-related small protein"""					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.304A>G	19.37:g.38795587A>G	ENSP00000301246:p.Lys102Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P6G2|Q96H58|Q9HCR4	Missense_Mutation	SNP	ENST00000301246.5	37	CCDS12511.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386721	0.25031	.	.	ENSG00000167644	ENST00000301246	.	.	.	4.65	1.27	0.21489	.	0.631638	0.14080	N	0.342742	T	0.26991	0.0661	L	0.32530	0.975	0.22710	N	0.99883	P	0.35507	0.506	B	0.37780	0.258	T	0.17531	-1.0366	9	0.87932	D	0	-18.943	6.8244	0.23874	0.7117:0.0:0.2883:0.0	.	102	Q9GZP8	IMUP_HUMAN	E	102	.	ENSP00000301246:K102E	K	+	1	0	C19orf33	43487427	0.981000	0.34729	0.010000	0.14722	0.004000	0.04260	1.231000	0.32624	0.282000	0.22254	0.459000	0.35465	AAG		0.602	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1		NM_033520	
EQTN	54586	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	27296984	27296984	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:27296984T>C	ENST00000380032.3	-	1	153	c.70A>G	c.(70-72)Att>Gtt	p.I24V	EQTN_ENST00000537675.1_Missense_Mutation_p.I24V|EQTN_ENST00000484994.1_5'Flank|EQTN_ENST00000380031.1_Missense_Mutation_p.I24V	NM_020641.2	NP_065692.2	Q9NQ60	EQTN_HUMAN	equatorin, sperm acrosome associated	24					acrosomal vesicle exocytosis (GO:0060478)|endocytosis (GO:0006897)|fusion of sperm to egg plasma membrane (GO:0007342)	early endosome (GO:0005769)|inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|outer acrosomal membrane (GO:0002081)|plasma membrane (GO:0005886)											TCACCTTCAATAGTAGGCTTC	0.308																																																	0													26.0	27.0	27.0					9																	27296984		2195	4295	6490	SO:0001583	missense	0			AJ278482	CCDS35001.1, CCDS55300.1	9p21	2012-09-20	2012-09-20	2012-09-20	ENSG00000120160	ENSG00000120160			1359	protein-coding gene	gene with protein product	"""Acr formation associated factor"", ""Acrosome formation associated factor"", ""sperm acrosome associated 8"""		"""chromosome 9 open reading frame 11"", ""equatorin"""	C9orf11			Standard	NM_020641		Approved	AFAF, SPACA8, equatorin	uc003zql.3	Q9NQ60	OTTHUMG00000021033	ENST00000380032.3:c.70A>G	9.37:g.27296984T>C	ENSP00000369371:p.Ile24Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPB3|B7ZMK1|Q5TCU1|Q96L22	Missense_Mutation	SNP	ENST00000380032.3	37	CCDS35001.1	.	.	.	.	.	.	.	.	.	.	T	0.667	-0.803598	0.02841	.	.	ENSG00000120160	ENST00000537675;ENST00000380032;ENST00000380031	T;T;T	0.28666	1.6;2.02;1.62	4.46	-8.93	0.00771	.	2.197700	0.01803	N	0.033005	T	0.10165	0.0249	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.23154	-1.0196	10	0.02654	T	1	.	4.6669	0.12670	0.2228:0.4711:0.1885:0.1176	.	24;24;24	B7ZMK1;Q9NQ60-2;Q9NQ60	.;.;AFAF_HUMAN	V	24	ENSP00000441630:I24V;ENSP00000369371:I24V;ENSP00000369370:I24V	ENSP00000369370:I24V	I	-	1	0	C9orf11	27286984	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.801000	0.00363	-2.969000	0.00287	-0.274000	0.10170	ATT		0.308	EQTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055499.1		NM_020641	
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:26245986A>T	ENST00000337620.4	+	3	452		c.e3-1		CBX3_ENST00000396386.2_Splice_Site|CBX3_ENST00000497498.1_Splice_Site|CBX3_ENST00000409747.1_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GTTTTATTTTAGCAAAAAATG	0.308																																																	0													32.0	33.0	32.0					7																	26245986		2200	4300	6500	SO:0001630	splice_region_variant	11335			U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.25-1A>T	7.37:g.26245986A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999549	0.54147	.	.	ENSG00000122565	ENST00000337620;ENST00000396386;ENST00000456948;ENST00000409747	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2344	0.54508	0.8582:0.1418:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26212511	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.092000	0.50207	2.323000	0.78572	0.533000	0.62120	.		0.308	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1		NM_007276	Intron
CCDC74A	90557	broad.mit.edu;hgsc.bcm.edu	37	2	132285695	132285695	+	Missense_Mutation	SNP	T	T	G	rs371462524		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:132285695T>G	ENST00000295171.6	+	1	290	c.152T>G	c.(151-153)cTg>cGg	p.L51R	CCDC74A_ENST00000409856.3_Missense_Mutation_p.L51R|CCDC74A_ENST00000467992.2_5'Flank|CCDC74A_ENST00000478665.1_3'UTR	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	51										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						AAACGGAACCTGGACCTGGAG	0.652																																																	0													44.0	42.0	43.0					2																	132285695		2203	4299	6502	SO:0001583	missense	90557				CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.152T>G	2.37:g.132285695T>G	ENSP00000295171:p.Leu51Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	16.33	3.092385	0.55968	.	.	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.38722	1.12;1.12	2.79	2.79	0.32731	.	0.536140	0.14692	U	0.304073	T	0.55449	0.1921	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.991	D;D;D	0.85130	0.934;0.997;0.955	T	0.47598	-0.9105	10	0.30854	T	0.27	-3.9273	8.821	0.35025	0.0:0.0:0.0:1.0	.	51;51;51	B4DZ94;Q96AQ1-2;Q96AQ1	.;.;CC74A_HUMAN	R	51	ENSP00000295171:L51R;ENSP00000387009:L51R	ENSP00000295171:L51R	L	+	2	0	CCDC74A	132002165	0.996000	0.38824	0.982000	0.44146	0.450000	0.32258	3.145000	0.50623	0.926000	0.37118	0.113000	0.15668	CTG		0.652	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2		NM_138770	
CD7	924	broad.mit.edu	37	17	80274162	80274162	+	Frame_Shift_Del	DEL	G	G	-	rs201027731|rs555569626	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:80274162delG	ENST00000312648.3	-	3	627	c.521delC	c.(520-522)ccafs	p.P174fs	CD7_ENST00000584284.1_Frame_Shift_Del_p.P174fs|CD7_ENST00000578509.1_Frame_Shift_Del_p.P74fs|CD7_ENST00000583376.1_Frame_Shift_Del_p.P74fs	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	174	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			AGAGGCTGCTGGCGGGTCAGG	0.716													?|GG|G|unsure	60	0.0119808	0.0008	0.0274	5008	,	,		11833	0.001		0.0338	False		,,,				2504	0.0051				Pancreas(45;804 1068 19702 28207 28798)												0													11.0	14.0	13.0					17																	80274162		2162	4241	6403	SO:0001589	frameshift_variant	924			X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1695	protein-coding gene	gene with protein product	"""p41 protein"", ""T-cell antigen CD7"", ""T-cell leukemia antigen"""	186820	"""CD7 antigen (p41)"""			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.521delC	17.37:g.80274162delG	ENSP00000312027:p.Pro174fs	Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Del	DEL	ENST00000312648.3	37	CCDS11807.1																																																																																				0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1		NM_006137	
CDC27	996	hgsc.bcm.edu	37	17	45234350	45234350	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:45234350C>T	ENST00000066544.3	-	7	864	c.771G>A	c.(769-771)caG>caA	p.Q257Q	CDC27_ENST00000531206.1_Silent_p.Q257Q|CDC27_ENST00000527547.1_Silent_p.Q257Q|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000446365.2_Silent_p.Q196Q	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	257					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.Q257Q(3)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TATTTTGAACCTGTTTAGATA	0.383																																																	3	Substitution - coding silent(3)	prostate(3)											57.0	63.0	61.0					17																	45234350		2198	4294	6492	SO:0001819	synonymous_variant	996			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.771G>A	17.37:g.45234350C>T		Somatic		WXS	Illumina HiSeq	Phase_I	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																				0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			
CDH7	1005	broad.mit.edu;ucsc.edu	37	18	63430106	63430106	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr18:63430106C>G	ENST00000397968.2	+	2	454	c.28C>G	c.(28-30)Cat>Gat	p.H10D	CDH7_ENST00000323011.3_Missense_Mutation_p.H10D|CDH7_ENST00000536984.2_Missense_Mutation_p.H10D	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	10					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				GGAGTTCTGCCATTTTCTGCA	0.413																																																	0													115.0	113.0	113.0					18																	63430106		2203	4300	6503	SO:0001583	missense	1005			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.28C>G	18.37:g.63430106C>G	ENSP00000381058:p.His10Asp	Somatic		WXS	Illumina GAIIx	Phase_I	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094974	0.36952	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.53640	0.61;0.62;0.61	5.83	5.83	0.93111	.	0.162003	0.44097	D	0.000493	T	0.44953	0.1318	L	0.44542	1.39	0.43777	D	0.996302	P;B	0.42785	0.79;0.118	B;B	0.39119	0.291;0.037	T	0.32455	-0.9906	10	0.37606	T	0.19	.	20.1195	0.97955	0.0:1.0:0.0:0.0	.	10;10	F5H5X9;Q9ULB5	.;CADH7_HUMAN	D	10	ENSP00000319166:H10D;ENSP00000443030:H10D;ENSP00000381058:H10D	ENSP00000319166:H10D	H	+	1	0	CDH7	61581086	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.252000	0.51461	2.759000	0.94783	0.650000	0.86243	CAT		0.413	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2		NM_033646	
CNGA2	1260	broad.mit.edu;ucsc.edu	37	X	150912325	150912325	+	Silent	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:150912325G>A	ENST00000329903.4	+	6	1383	c.1350G>A	c.(1348-1350)aaG>aaA	p.K450K		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	450					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					CCACACTCAAGAAAGTGCGCA	0.507																																																	0													84.0	79.0	81.0					X																	150912325		2203	4300	6503	SO:0001819	synonymous_variant	1260			S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1350G>A	X.37:g.150912325G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A0AVD0	Silent	SNP	ENST00000329903.4	37	CCDS14701.1																																																																																				0.507	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1		NM_005140	
CYFIP1	23191	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	22928512	22928512	+	Splice_Site	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:22928512T>C	ENST00000313077.7	+	5	512		c.e5+2		CYFIP1_ENST00000560848.1_Splice_Site	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TACTTCCAGGTAAAATGGCAA	0.493																																																	0													72.0	79.0	77.0					15																	22928512		2203	4300	6503	SO:0001630	splice_region_variant	23191			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.387+2T>C	15.37:g.22928512T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Splice_Site	SNP	ENST00000313077.7	37	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.988964	0.74589	.	.	ENSG00000068793	ENST00000313077;ENST00000412127	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5679	0.68191	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CYFIP1	20479953	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.668000	0.83897	2.035000	0.60131	0.454000	0.30748	.		0.493	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2		NM_014608	Intron
DDX11	1663	hgsc.bcm.edu	37	12	31242358	31242358	+	Missense_Mutation	SNP	G	G	A	rs199585751		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:31242358G>A	ENST00000407793.2	+	8	1065	c.814G>A	c.(814-816)Gtg>Atg	p.V272M	DDX11_ENST00000545668.1_Missense_Mutation_p.V272M|DDX11_ENST00000228264.6_Missense_Mutation_p.V246M|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.V272M|DDX11_ENST00000350437.4_Missense_Mutation_p.V272M	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	272	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AAATGAAGACGTGAAAAGCCT	0.522										Multiple Myeloma(12;0.14)																																							0													87.0	86.0	86.0					12																	31242358		2203	4300	6503	SO:0001583	missense	1663			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.814G>A	12.37:g.31242358G>A	ENSP00000384703:p.Val272Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.444369	0.43429	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000228264;ENST00000438391;ENST00000545668;ENST00000350437	T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	3.3	1.43	0.22495	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	H	0.97186	3.955	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.85977	0.1480	10	0.87932	D	0	.	7.1353	0.25525	0.2356:0.0:0.7644:0.0	.	272;272;272	Q96FC9;Q96FC9-4;Q96FC9-2	DDX11_HUMAN;.;.	M	272;272;246;243;272;272	ENSP00000443426:V272M;ENSP00000384703:V272M;ENSP00000228264:V246M;ENSP00000407646:V243M;ENSP00000440402:V272M;ENSP00000309965:V272M	ENSP00000228264:V246M	V	+	1	0	DDX11	31133625	1.000000	0.71417	0.002000	0.10522	0.000000	0.00434	8.747000	0.91610	0.132000	0.18615	-0.424000	0.05967	GTG		0.522	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1		NM_030653	
DNAH9	1770	hgsc.bcm.edu;ucsc.edu	37	17	11795233	11795233	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:11795233A>T	ENST00000262442.4	+	58	11320	c.11252A>T	c.(11251-11253)aAg>aTg	p.K3751M	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Missense_Mutation_p.K63M|DNAH9_ENST00000454412.2_Missense_Mutation_p.K3751M	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3751					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGTGTGATAAGCTGACCTAC	0.488																																																	0													160.0	157.0	158.0					17																	11795233		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11252A>T	17.37:g.11795233A>T	ENSP00000262442:p.Lys3751Met	Somatic		WXS	Illumina HiSeq	Phase_I	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.611365	0.87258	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001;ENST00000361801	T;T;T	0.77620	-1.11;-1.11;-1.11	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.93527	0.7934	H	0.99454	4.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.96268	0.9196	10	0.87932	D	0	.	15.6785	0.77349	1.0:0.0:0.0:0.0	.	104;3751	B7Z7H0;Q9NYC9	.;DYH9_HUMAN	M	3751;3751;2333;63;104	ENSP00000262442:K3751M;ENSP00000414874:K3751M;ENSP00000379323:K63M	ENSP00000262442:K3751M	K	+	2	0	DNAH9	11735958	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.079000	0.94032	2.288000	0.76882	0.533000	0.62120	AAG		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
EBPL	84650	broad.mit.edu	37	13	50235160	50235160	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr13:50235160G>C	ENST00000242827.6	-	4	615	c.565C>G	c.(565-567)Cta>Gta	p.L189V	EBPL_ENST00000378272.5_3'UTR|EBPL_ENST00000378284.2_3'UTR|EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378270.5_3'UTR	NM_032565.3	NP_115954.1	Q9BY08	EBPL_HUMAN	emopamil binding protein-like	189					sterol metabolic process (GO:0016125)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholestenol delta-isomerase activity (GO:0047750)	p.L189V(9)		endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		TTGAGTTCTAGCCATGACTGC	0.418																																					NSCLC(39;857 1083 36109 42364 51411)												9	Substitution - Missense(9)	endometrium(6)|kidney(3)											67.0	67.0	67.0					13																	50235160		2203	4300	6503	SO:0001583	missense	84650			AF243433	CCDS9420.1, CCDS61334.1	13q12-q13	2008-02-05			ENSG00000123179	ENSG00000123179			18061	protein-coding gene	gene with protein product							Standard	NM_032565		Approved	EBRP	uc001vdg.3	Q9BY08	OTTHUMG00000016920	ENST00000242827.6:c.565C>G	13.37:g.50235160G>C	ENSP00000242827:p.Leu189Val	Somatic		WXS	Illumina GAIIx	Phase_I	A6NJ59|Q569H7|Q5JVN2|Q5JVN3|Q5JVN4|Q5JVN5|Q5JVN6	Missense_Mutation	SNP	ENST00000242827.6	37	CCDS9420.1	.	.	.	.	.	.	.	.	.	.	C	3.076	-0.189988	0.06299	.	.	ENSG00000123179	ENST00000242827	D	0.97850	-4.57	5.61	2.84	0.33178	.	0.689671	0.14945	N	0.289287	D	0.88179	0.6367	N	0.00621	-1.32	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.79482	-0.1785	10	0.25751	T	0.34	-0.2032	8.3049	0.32036	0.0:0.4998:0.3595:0.1406	.	189	Q9BY08	EBPL_HUMAN	V	189	ENSP00000242827:L189V	ENSP00000242827:L189V	L	-	1	2	EBPL	49133161	0.000000	0.05858	0.303000	0.25071	0.899000	0.52679	-1.071000	0.03437	0.397000	0.25310	-0.127000	0.14921	CTA		0.418	EBPL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044932.2		NM_032565	
EPPK1	83481	hgsc.bcm.edu	37	8	144940649	144940649	+	Missense_Mutation	SNP	G	G	A	rs200167763		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr8:144940649G>A	ENST00000525985.1	-	2	6844	c.6773C>T	c.(6772-6774)aCg>aTg	p.T2258M				P58107	EPIPL_HUMAN	epiplakin 1	2258						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CACCAGGGCCGTGCCGGGCCG	0.726																																																	0													45.0	43.0	44.0					8																	144940649		2162	4251	6413	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6773C>T	8.37:g.144940649G>A	ENSP00000436337:p.Thr2258Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	G	27.2	4.814048	0.90790	.	.	ENSG00000227184	ENST00000525985	T	0.74421	-0.84	4.67	4.67	0.58626	.	.	.	.	.	D	0.87014	0.6072	M	0.85299	2.745	0.49483	D	0.999795	D	0.89917	1.0	D	0.97110	1.0	D	0.88917	0.3363	9	0.66056	D	0.02	.	15.1226	0.72457	0.0:0.0:1.0:0.0	.	2258	E9PPU0	.	M	2258	ENSP00000436337:T2258M	ENSP00000436337:T2258M	T	-	2	0	EPPK1	145012637	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.403000	0.73264	2.420000	0.82092	0.591000	0.81541	ACG		0.726	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1		NM_031308	
EPS8	2059	broad.mit.edu	37	12	15803929	15803929	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:15803929G>A	ENST00000281172.5	-	14	1698	c.1262C>T	c.(1261-1263)cCa>cTa	p.P421L	EPS8_ENST00000543612.1_Missense_Mutation_p.P421L|EPS8_ENST00000542903.1_Missense_Mutation_p.P161L|EPS8_ENST00000540613.1_Missense_Mutation_p.P161L|EPS8_ENST00000543523.1_Missense_Mutation_p.P421L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	421	Pro-rich.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CTGTTCTTTTGGCCACTCTGC	0.433																																																	0													104.0	103.0	103.0					12																	15803929		2203	4300	6503	SO:0001583	missense	2059			U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.1262C>T	12.37:g.15803929G>A	ENSP00000281172:p.Pro421Leu	Somatic		WXS	Illumina GAIIx	Phase_I	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	37	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306906	0.81247	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903;ENST00000543223	T;T;T;T;T	0.08896	3.11;3.11;3.11;3.04;3.04	5.52	5.52	0.82312	.	0.052846	0.85682	D	0.000000	T	0.32763	0.0840	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.04140	-1.0974	10	0.87932	D	0	-11.7315	17.6108	0.88053	0.0:0.0:1.0:0.0	.	421	Q12929	EPS8_HUMAN	L	421;421;421;161;161;421	ENSP00000441867:P421L;ENSP00000281172:P421L;ENSP00000442388:P421L;ENSP00000441888:P161L;ENSP00000437806:P161L	ENSP00000281172:P421L	P	-	2	0	EPS8	15695196	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	9.223000	0.95203	2.579000	0.87056	0.650000	0.86243	CCA		0.433	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			
ERBB2	2064	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	37873629	37873629	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:37873629C>T	ENST00000269571.5	+	15	1953	c.1794C>T	c.(1792-1794)gcC>gcT	p.A598A	ERBB2_ENST00000540042.1_Silent_p.A568A|ERBB2_ENST00000541774.1_Silent_p.A583A|ERBB2_ENST00000584450.1_Silent_p.A598A|ERBB2_ENST00000445658.2_Silent_p.A322A|ERBB2_ENST00000584601.1_Silent_p.A568A|ERBB2_ENST00000406381.2_Silent_p.A568A|ERBB2_ENST00000540147.1_Silent_p.A568A|ERBB2_ENST00000578199.1_Silent_p.A568A			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	598					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TCTGCGTGGCCCGCTGCCCCA	0.622		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																														Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	0													52.0	49.0	50.0					17																	37873629		2203	4300	6503	SO:0001819	synonymous_variant	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1794C>T	17.37:g.37873629C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																				0.622	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			
ESYT3	83850	hgsc.bcm.edu;ucsc.edu	37	3	138170931	138170942	+	Splice_Site	DEL	GGTAAGGCCGCT	GGTAAGGCCGCT	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	GGTAAGGCCGCT	GGTAAGGCCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr3:138170931_138170942delGGTAAGGCCGCT	ENST00000389567.4	+	2	555	c.369delGGTAAGGCCGCT	c.(367-369)aag>aa	p.K123del	ESYT3_ENST00000289135.4_Splice_Site_p.K123del	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	123	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						GGGCCAACAAGGTAAGGCCGCTGGCAGGGCCT	0.656																																																	0																																										SO:0001630	splice_region_variant	83850			AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"""Synaptotagmins"""	24295	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member C"""	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.369+1GGTAAGGCCGCT>-	3.37:g.138170931_138170942delGGTAAGGCCGCT		Somatic		WXS	Illumina HiSeq	Phase_I	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Frame_Shift_Del	DEL	ENST00000389567.4	37	CCDS3101.2																																																																																				0.656	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1		NM_031913	In_Frame_Del
FAM186A	121006	hgsc.bcm.edu	37	12	50746022	50746022	+	Silent	SNP	C	C	G	rs7304692	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:50746022C>G	ENST00000327337.5	-	4	4592	c.4593G>C	c.(4591-4593)ctG>ctC	p.L1531L	FAM186A_ENST00000543111.1_Silent_p.L1531L|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1531								p.L1531L(1)									GCGGAGGGATCAGAGGGATCC	0.652													-|||	112	0.0223642	0.0484	0.0086	5008	,	,		17334	0.0327		0.004	False		,,,				2504	0.0051				NSCLC(138;1796 1887 12511 19463 37884)												1	Substitution - coding silent(1)	lung(1)											9.0	9.0	9.0					12																	50746022		690	1591	2281	SO:0001819	synonymous_variant	121006				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4593G>C	12.37:g.50746022C>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																				0.652	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1		XM_001718353	
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:19184746_19184747insTCT	ENST00000275461.3	-	1	297_298	c.239_240insAGA	c.(238-240)gag>gaAGAg	p.80_80E>EE	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	80	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E81_R82insE(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ttccgcgctcctcttcctcctc	0.624														836	0.166933	0.0446	0.1643	5008	,	,		17679	0.1587		0.2654	False		,,,				2504	0.2413																1	Insertion - In frame(1)	ovary(1)								307,0,3957		13,0,281,0,0,1838						0.6	0.7		dbSNP_134	60	2211,1,6042		291,0,1629,0,1,2206	no	codingComplex	FERD3L	NM_152898.2		304,0,1910,0,1,4044	A1A1,A1A2,A1R,A2A2,A2R,RR		26.7991,7.1998,20.123				2518,1,9999				SO:0001652	inframe_insertion	222894			AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.237_239dupAGA	7.37:g.19184747_19184749dupTCT	ENSP00000275461:p.Glu81dup	Somatic		WXS	Illumina HiSeq	Phase_I	Q495K0	In_Frame_Ins	INS	ENST00000275461.3	37	CCDS5368.1																																																																																				0.624	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			
ANKRD36BP2	645784	broad.mit.edu	37	2	89100619	89100619	+	RNA	SNP	C	C	T	rs75347118		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:89100619C>T	ENST00000393525.3	+	0	1093									ankyrin repeat domain 36B pseudogene 2																		TCAACAGCAACTGGATGATGC	0.373																																																	0																																												0					2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89100619C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000393525.3	37																																																																																					0.373	ANKRD36BP2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000323523.1			
GART	2618	hgsc.bcm.edu	37	21	34882122	34882122	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr21:34882122delT	ENST00000381831.3	-	18	2683	c.2420delA	c.(2419-2421)aagfs	p.K807fs	GART_ENST00000381815.4_Frame_Shift_Del_p.K807fs|GART_ENST00000543717.1_Frame_Shift_Del_p.K359fs|GART_ENST00000381839.3_Frame_Shift_Del_p.K807fs	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	807	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.K807fs*7(2)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	CACTCTGGCCTTTTTTTTTTC	0.448																																																	2	Deletion - Frameshift(2)	ovary(2)							,,	89,4175		15,59,2058	66.0	70.0	68.0		,,	1.6	0.9	21		70	96,8158		13,70,4044	no	frameshift,frameshift,frameshift	GART	NM_001136006.1,NM_001136005.1,NM_000819.4	,,	28,129,6102	A1A1,A1R,RR		1.1631,2.0872,1.4779	,,	,,	34882122	185,12333	2203	4300	6503	SO:0001589	frameshift_variant	2618			M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2420delA	21.37:g.34882122delT	ENSP00000371253:p.Lys807fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Frame_Shift_Del	DEL	ENST00000381831.3	37	CCDS13627.1																																																																																				0.448	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3		NM_000819	
GH2	2689	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	61958132	61958132	+	Splice_Site	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:61958132C>G	ENST00000423893.2	-	4	517	c.456G>C	c.(454-456)tgG>tgC	p.W152C	GH2_ENST00000332800.7_Missense_Mutation_p.W152C|GH2_ENST00000449787.2_Splice_Site_p.W137C|GH2_ENST00000456543.2_Intron			P01242	SOM2_HUMAN	growth hormone 2	152					JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						CCACCCTCACCCACATCAGCG	0.602																																																	0													88.0	86.0	86.0					17																	61958132		2203	4300	6503	SO:0001630	splice_region_variant	2689			J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"""Endogenous ligands"""	4262	protein-coding gene	gene with protein product	"""placental-specific growth hormone"", ""placenta-specific growth hormone"""	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.456+1G>C	17.37:g.61958132C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	.	.	.	.	.	.	.	.	.	.	c	11.93	1.785546	0.31593	.	.	ENSG00000136487	ENST00000332800;ENST00000423893;ENST00000449787	D;D;D	0.88586	-2.4;-2.17;-2.17	2.94	2.94	0.34122	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.497073	0.21017	N	0.081586	D	0.87958	0.6309	L	0.29908	0.895	0.39141	D	0.962035	B;B;D	0.54207	0.363;0.427;0.965	P;B;P	0.56343	0.656;0.401;0.796	D	0.89238	0.3582	10	0.72032	D	0.01	.	11.7079	0.51607	0.0:1.0:0.0:0.0	.	152;137;152	P01242;O14643;B1A4H7	SOM2_HUMAN;.;.	C	152;152;137	ENSP00000333157:W152C;ENSP00000409294:W152C;ENSP00000410618:W137C	ENSP00000333157:W152C	W	-	3	0	GH2	59311864	1.000000	0.71417	0.999000	0.59377	0.088000	0.18126	3.545000	0.53648	1.644000	0.50603	0.306000	0.20318	TGG		0.602	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1		NM_002059	Missense_Mutation
GOLGA6L3	100133220	broad.mit.edu	37	15	83014106	83014106	+	Silent	SNP	T	T	C	rs62009901		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:83014106T>C	ENST00000557886.1	-	6	576	c.477A>G	c.(475-477)gtA>gtG	p.V159V															p.V159V(12)		endometrium(6)|kidney(5)|prostate(1)	12						GTAGCTGCTCTACCTTAGATG	0.498																																																	12	Substitution - coding silent(12)	kidney(6)|endometrium(4)|prostate(2)																																								SO:0001819	synonymous_variant	647042																														ENST00000557886.1:c.477A>G	15.37:g.83014106T>C		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000557886.1	37																																																																																					0.498	RP13-996F3.4-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419277.1			
GOLGA6L5P	374650	broad.mit.edu	37	15	85056047	85056047	+	RNA	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:85056047C>G	ENST00000560239.1	-	0	984				GOLGA6L5_ENST00000414190.2_RNA																							GCTGGGGGCTCTGGGGCCAGG	0.527																																																	0																																												374650																															15.37:g.85056047C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000560239.1	37																																																																																					0.527	RP11-182J1.12-001	KNOWN	mRNA_end_NF|basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000418581.1			
GPR179	440435	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	36482951	36482951	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:36482951T>G	ENST00000342292.4	-	11	6521	c.6501A>C	c.(6499-6501)gaA>gaC	p.E2167D	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2167					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TTGAGAAGTGTTCTTCCGTCC	0.597																																																	0													113.0	116.0	115.0					17																	36482951		2098	4224	6322	SO:0001583	missense	440435				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.6501A>C	17.37:g.36482951T>G	ENSP00000345060:p.Glu2167Asp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	T	9.613	1.131693	0.21041	.	.	ENSG00000188888	ENST00000342292	T	0.52057	0.68	4.55	-1.95	0.07548	.	0.000000	0.35838	N	0.002950	T	0.34279	0.0892	L	0.55481	1.735	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.17561	-1.0365	10	0.52906	T	0.07	-3.9221	4.6298	0.12496	0.0:0.2499:0.2972:0.453	.	2167	Q6PRD1	GP179_HUMAN	D	2167	ENSP00000345060:E2167D	ENSP00000345060:E2167D	E	-	3	2	GPR179	33736477	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.089000	0.15002	-0.647000	0.05444	-0.467000	0.05162	GAA		0.597	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			
H2AFV	94239	hgsc.bcm.edu	37	7	44874131	44874131	+	Missense_Mutation	SNP	A	A	G	rs114398265		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:44874131A>G	ENST00000308153.4	-	5	447	c.356T>C	c.(355-357)aTt>aCt	p.I119T	H2AFV_ENST00000521529.1_3'UTR|H2AFV_ENST00000349299.3_Missense_Mutation_p.I81T|H2AFV_ENST00000350771.3_Missense_Mutation_p.I93T|H2AFV_ENST00000381124.5_3'UTR|H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000222690.6_Intron	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	119						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I119T(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						CTTCTTTCCAATCAGAGATTT	0.368																																																	1	Substitution - Missense(1)	prostate(1)											88.0	76.0	80.0					7																	44874131		2203	4300	6503	SO:0001583	missense	94239			AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.356T>C	7.37:g.44874131A>G	ENSP00000308405:p.Ile119Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801702	0.50315	.	.	ENSG00000105968	ENST00000349299;ENST00000308153;ENST00000350771	T;D;T	0.83163	0.93;-1.69;0.89	5.61	5.61	0.85477	Histone-fold (1);Histone H2A (2);	.	.	.	.	D	0.82444	0.5038	M	0.69523	2.12	0.80722	D	1	B;B;B	0.17852	0.001;0.024;0.0	B;B;B	0.18871	0.005;0.023;0.001	T	0.80027	-0.1554	9	0.62326	D	0.03	-10.9595	14.0456	0.64704	1.0:0.0:0.0:0.0	.	93;81;119	A6NKY0;A6NFA8;Q71UI9	.;.;H2AV_HUMAN	T	81;119;93	ENSP00000342714:I81T;ENSP00000308405:I119T;ENSP00000340708:I93T	ENSP00000308405:I119T	I	-	2	0	H2AFV	44840656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.631000	0.90991	2.261000	0.74972	0.533000	0.62120	ATT		0.368	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1		NM_012412	
HLA-C	3107	hgsc.bcm.edu	37	6	31237802	31237802	+	Missense_Mutation	SNP	A	A	G	rs1050147	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:31237802A>G	ENST00000376228.5	-	5	970	c.956T>C	c.(955-957)gTt>gCt	p.V319A	HLA-C_ENST00000383329.3_Missense_Mutation_p.V319A	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	325					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGCTAGGACAACCAGGACAGC	0.597																																																	0								G	ALA/VAL	3060,1334		1314,432,451	46.0	47.0	47.0		956	-0.2	0.0	6	dbSNP_123	47	5060,3518		1977,1106,1206	yes	missense	HLA-C	NM_002117.5	64	3291,1538,1657	GG,GA,AA		41.0119,30.3596,37.4036	benign	319/367	31237802	8120,4852	2197	4289	6486	SO:0001583	missense	3107			M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.956T>C	6.37:g.31237802A>G	ENSP00000365402:p.Val319Ala	Somatic		WXS	Illumina HiSeq	Phase_I	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	1682	0.7701465201465202	392	0.7967479674796748	291	0.8038674033149171	456	0.7972027972027972	543	0.716358839050132	.	0.012	-1.691464	0.00731	0.696404	0.589881	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00958	5.52;5.5	0.109	-0.218	0.13142	.	0.672928	0.11860	N	0.522519	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.43925	-0.9361	7	0.21540	T	0.41	.	.	.	.	rs17413387;rs35376379;rs41553619	319;319;319;319	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	A	319;319;319;356	ENSP00000365402:V319A;ENSP00000372819:V319A	ENSP00000365402:V319A	V	-	2	0	HLA-C	31345781	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.742000	0.01835	-2.815000	0.00346	-2.811000	0.00111	GTT		0.597	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3		NM_002117	
HLA-B	3106	hgsc.bcm.edu	37	6	31323128	31323128	+	Silent	SNP	A	A	G	rs41551014		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:31323128A>G	ENST00000412585.2	-	4	889	c.861T>C	c.(859-861)caT>caC	p.H287H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	287	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCAGCCCCTCATGCTGTACAT	0.572									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																																								0													67.0	61.0	63.0					6																	31323128		2203	4300	6503	SO:0001819	synonymous_variant	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.861T>C	6.37:g.31323128A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																				0.572	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4		NM_005514	
HLA-B	3106	hgsc.bcm.edu	37	6	31323143	31323143	+	Silent	SNP	T	T	C	rs41546016		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:31323143T>C	ENST00000412585.2	-	4	874	c.846A>G	c.(844-846)acA>acG	p.T282T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	282	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GTACATGGCATGTGTATCTCT	0.572									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																																								0													80.0	69.0	73.0					6																	31323143		2203	4300	6503	SO:0001819	synonymous_variant	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.846A>G	6.37:g.31323143T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																				0.572	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4		NM_005514	
HLA-B	3106	hgsc.bcm.edu	37	6	31323202	31323202	+	Missense_Mutation	SNP	T	T	C	rs41545916		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:31323202T>C	ENST00000412585.2	-	4	815	c.787A>G	c.(787-789)Aga>Gga	p.R263G		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	263	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGGAAGGTTCTATCTCCTGCT	0.582									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																																								0													93.0	79.0	84.0					6																	31323202		2203	4300	6503	SO:0001583	missense	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.787A>G	6.37:g.31323202T>C	ENSP00000399168:p.Arg263Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	6.971	0.549058	0.13312	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.02323	4.34	3.16	1.33	0.21861	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.165679	0.27881	N	0.017476	T	0.00109	0.0003	N	0.00006	-3.21	0.25657	N	0.986046	B	0.06786	0.001	B	0.04013	0.001	T	0.24764	-1.0151	10	0.02654	T	1	.	7.8568	0.29487	0.0:0.778:0.0:0.222	rs41545916	263	P01889	1B07_HUMAN	G	263;142;142	ENSP00000399168:R263G	ENSP00000399168:R263G	R	-	1	2	HLA-B	31431181	0.310000	0.24527	0.455000	0.27031	0.099000	0.18886	0.951000	0.29135	0.182000	0.20032	-0.549000	0.04216	AGA		0.582	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4		NM_005514	
HLA-B	3106	hgsc.bcm.edu	37	6	31323215	31323215	+	Silent	SNP	T	T	C	rs41541216	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:31323215T>C	ENST00000412585.2	-	4	802	c.774A>G	c.(772-774)agA>agG	p.R258R		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	258	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTCCTGCTGGTCTGGTCTCCA	0.582									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																																								0													103.0	88.0	93.0					6																	31323215		2203	4300	6503	SO:0001819	synonymous_variant	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.774A>G	6.37:g.31323215T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																				0.582	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4		NM_005514	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376840	168376840	+	lincRNA	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr6:168376840T>C	ENST00000538528.1	-	0	779																											AGTGTGTGTGTGGGGAGCAGG	0.602																																																	0													31.0	29.0	30.0					6																	168376840		692	1591	2283			100128124																															6.37:g.168376840T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.602	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
HPS5	11234	broad.mit.edu;ucsc.edu	37	11	18327003	18327003	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:18327003G>A	ENST00000349215.3	-	8	1139	c.862C>T	c.(862-864)Cag>Tag	p.Q288*	HPS5_ENST00000396253.3_Nonsense_Mutation_p.Q174*|HPS5_ENST00000531848.1_Nonsense_Mutation_p.Q174*|HPS5_ENST00000438420.2_Nonsense_Mutation_p.Q174*	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	288					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GACAAAGACTGGGAGGATCCA	0.338									Hermansky-Pudlak syndrome																																								0													95.0	92.0	93.0					11																	18327003		2199	4293	6492	SO:0001587	stop_gained	11234	Familial Cancer Database	HPS, HPS1-8	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.862C>T	11.37:g.18327003G>A	ENSP00000265967:p.Gln288*	Somatic		WXS	Illumina GAIIx	Phase_I	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Nonsense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	G	39	7.593815	0.98378	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	.	.	.	5.67	5.67	0.87782	.	0.161057	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	19.1236	0.93374	0.0:0.0:1.0:0.0	.	.	.	.	X	174;174;288;174	.	ENSP00000265967:Q288X	Q	-	1	0	HPS5	18283579	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.011000	0.76359	2.833000	0.97629	0.585000	0.79938	CAG		0.338	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1		NM_181507	
HRC	3270	hgsc.bcm.edu	37	19	49657754	49657754	+	Silent	SNP	G	G	A	rs567490515	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:49657754G>A	ENST00000252825.4	-	1	927	c.741C>T	c.(739-741)gaC>gaT	p.D247D	HRC_ENST00000595625.1_Silent_p.D247D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	247	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		catcatcatcgtcatcttctt	0.507													G|||	238	0.047524	0.053	0.0476	5008	,	,		25432	0.0169		0.0417	False		,,,				2504	0.0777				Melanoma(37;75 1097 24567 25669 30645)												0													127.0	92.0	104.0					19																	49657754		2203	4300	6503	SO:0001819	synonymous_variant	3270				CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.741C>T	19.37:g.49657754G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																				0.507	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1		NM_002152	
IRS1	3667	broad.mit.edu	37	2	227660037	227660037	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:227660037G>A	ENST00000305123.5	-	1	4438	c.3418C>T	c.(3418-3420)Cgc>Tgc	p.R1140C	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	1140					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GAGCTGTGGCGTTTCACATCC	0.647																																																	0													41.0	44.0	43.0					2																	227660037		2203	4300	6503	SO:0001583	missense	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.3418C>T	2.37:g.227660037G>A	ENSP00000304895:p.Arg1140Cys	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226478	0.79576	.	.	ENSG00000169047	ENST00000305123	T	0.62788	0.0	5.81	5.81	0.92471	.	0.000000	0.64402	D	0.000003	T	0.61324	0.2338	L	0.59436	1.845	0.58432	D	0.999999	D	0.61697	0.99	B	0.43623	0.425	T	0.66984	-0.5785	10	0.66056	D	0.02	-22.8699	14.5185	0.67835	0.0:0.0:0.8533:0.1467	.	1140	P35568	IRS1_HUMAN	C	1140	ENSP00000304895:R1140C	ENSP00000304895:R1140C	R	-	1	0	IRS1	227368281	0.769000	0.28531	0.996000	0.52242	0.924000	0.55760	1.018000	0.30002	2.733000	0.93635	0.655000	0.94253	CGC		0.647	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3		NM_005544	
ITGA11	22801	broad.mit.edu;hgsc.bcm.edu	37	15	68595444	68595444	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:68595444G>C	ENST00000315757.7	-	30	3606	c.3520C>G	c.(3520-3522)Cgc>Ggc	p.R1174G	RP11-709B3.2_ENST00000569808.1_lincRNA|ITGA11_ENST00000423218.2_Missense_Mutation_p.R1175G	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1174	Poly-Arg.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TCCCTCCTGCGCCTGGCACTT	0.617																																																	0													18.0	21.0	20.0					15																	68595444		1829	3929	5758	SO:0001583	missense	22801			AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.3520C>G	15.37:g.68595444G>C	ENSP00000327290:p.Arg1174Gly	Somatic		WXS	Illumina HiSeq	Phase_I	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721921	0.68959	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.61392	0.11;0.11	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.70081	0.3183	M	0.70595	2.14	0.44627	D	0.997608	B;D	0.64830	0.04;0.994	B;P	0.57425	0.011;0.82	T	0.74819	-0.3535	10	0.72032	D	0.01	.	14.4829	0.67594	0.0:0.0:1.0:0.0	.	1174;1174	A8K8T0;Q9UKX5	.;ITA11_HUMAN	G	1174;1175;809	ENSP00000327290:R1174G;ENSP00000403392:R1175G	ENSP00000327290:R1174G	R	-	1	0	ITGA11	66382498	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.287000	0.59001	2.187000	0.69744	0.462000	0.41574	CGC		0.617	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_012211	
KCND2	3751	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	119915314	119915314	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:119915314G>A	ENST00000331113.4	+	1	1593	c.628G>A	c.(628-630)Gga>Aga	p.G210R		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	210					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AGTGCCGTGCGGATCAAGCCC	0.547																																																	0													116.0	106.0	110.0					7																	119915314		2203	4300	6503	SO:0001583	missense	3751			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.628G>A	7.37:g.119915314G>A	ENSP00000333496:p.Gly210Arg	Somatic		WXS	Illumina HiSeq	Phase_I	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.938175	0.34189	.	.	ENSG00000184408	ENST00000331113	D	0.96745	-4.11	5.58	5.58	0.84498	.	0.060515	0.64402	N	0.000004	D	0.95818	0.8639	M	0.78285	2.405	0.80722	D	1	B	0.18863	0.031	B	0.12837	0.008	D	0.93260	0.6642	9	.	.	.	.	19.5831	0.95478	0.0:0.0:1.0:0.0	.	210	Q9NZV8	KCND2_HUMAN	R	210	ENSP00000333496:G210R	.	G	+	1	0	KCND2	119702550	1.000000	0.71417	0.951000	0.38953	0.289000	0.27227	7.876000	0.87215	2.641000	0.89580	0.563000	0.77884	GGA		0.547	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1		NM_012281	
KIAA0368	23392	broad.mit.edu	37	9	114145539	114145539	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:114145539A>G	ENST00000338205.5	-	34	3974	c.3755T>C	c.(3754-3756)cTt>cCt	p.L1252P	KIAA0368_ENST00000374378.3_5'UTR|KIAA0368_ENST00000259335.4_Missense_Mutation_p.L1430P			Q5VYK3	ECM29_HUMAN	KIAA0368	1258					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TTTGTCCAGAAGGCAAGGCAG	0.498																																																	0													61.0	63.0	62.0					9																	114145539		2035	4176	6211	SO:0001583	missense	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.3755T>C	9.37:g.114145539A>G	ENSP00000339889:p.Leu1252Pro	Somatic		WXS	Illumina GAIIx	Phase_I	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	A	26.4	4.736486	0.89482	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.75050	-0.9	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.88760	0.6524	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91015	0.4853	10	0.87932	D	0	.	16.1852	0.81946	1.0:0.0:0.0:0.0	.	727	B3KXF2	.	P	1252;1430;727	ENSP00000259335:L1430P	ENSP00000259335:L1430P	L	-	2	0	KIAA0368	113185360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.649000	0.91067	2.277000	0.76020	0.528000	0.53228	CTT		0.498	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2		NM_014686	
KLHL6	89857	broad.mit.edu;hgsc.bcm.edu	37	3	183217550	183217550	+	Silent	SNP	G	G	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr3:183217550G>T	ENST00000341319.3	-	4	1010	c.975C>A	c.(973-975)ggC>ggA	p.G325G		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	325					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			TCGTGCAGCCGCCAATGATCA	0.582																																																	0													76.0	63.0	67.0					3																	183217550		2203	4300	6503	SO:0001819	synonymous_variant	89857			AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.975C>A	3.37:g.183217550G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																				0.582	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1		NM_130446	
KRT3	3850	hgsc.bcm.edu	37	12	53189410	53189410	+	Silent	SNP	A	A	C	rs529558333	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:53189410A>C	ENST00000417996.2	-	1	491	c.417T>G	c.(415-417)ggT>ggG	p.G139G	KRT3_ENST00000309505.3_Silent_p.G139G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	139	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						agccaccaggaccaccaaagc	0.632													A|||	15	0.00299521	0.0023	0.0014	5008	,	,		10730	0.0069		0.001	False		,,,				2504	0.0031																0													158.0	201.0	186.0					12																	53189410		2182	4268	6450	SO:0001819	synonymous_variant	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.417T>G	12.37:g.53189410A>C		Somatic		WXS	Illumina HiSeq	Phase_I	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																				0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1		NM_057088	
KRT3	3850	hgsc.bcm.edu	37	12	53189427	53189427	+	Missense_Mutation	SNP	C	C	G	rs148531142		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:53189427C>G	ENST00000417996.2	-	1	474	c.400G>C	c.(400-402)Gct>Cct	p.A134P	KRT3_ENST00000309505.3_Missense_Mutation_p.A134P	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	134	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						aagccaccagcccctccaaag	0.632																																																	0													141.0	187.0	172.0					12																	53189427		2178	4256	6434	SO:0001583	missense	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.400G>C	12.37:g.53189427C>G	ENSP00000413479:p.Ala134Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	c	6.997	0.554067	0.13374	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.85171	-1.95;-1.95	3.45	0.361	0.16107	.	0.198436	0.24869	N	0.034957	T	0.76428	0.3986	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.61446	-0.7061	10	0.33940	T	0.23	.	7.7249	0.28755	0.1722:0.493:0.3348:0.0	.	134	P12035	K2C3_HUMAN	P	134	ENSP00000413479:A134P;ENSP00000312206:A134P	ENSP00000312206:A134P	A	-	1	0	KRT3	51475694	0.000000	0.05858	0.001000	0.08648	0.428000	0.31595	-0.074000	0.11450	-0.174000	0.10743	0.603000	0.83216	GCT		0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1		NM_057088	
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340729	39340729	+	Silent	SNP	G	G	A	rs373304706		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:39340729G>A	ENST00000398472.1	-	1	865	c.378C>T	c.(376-378)tgC>tgT	p.C126C				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	126	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			TGGTCTGACAGCAGAGTGGAC	0.602																																																	0													86.0	94.0	92.0					17																	39340729		2171	4277	6448	SO:0001819	synonymous_variant	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.378C>T	17.37:g.39340729G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8MWS7|Q3SYF2	Silent	SNP	ENST00000398472.1	37																																																																																					0.602	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1		NM_033060	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642703	1642703	+	Silent	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1642703A>G	ENST00000399682.1	-	1	665	c.621T>C	c.(619-621)agT>agC	p.S207S		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GATTGCAGCAACTGGACTGGC	0.592																																																	0													88.0	79.0	82.0					11																	1642703		692	1591	2283	SO:0001819	synonymous_variant	387267			AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.621T>C	11.37:g.1642703A>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000399682.1	37																																																																																					0.592	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1		NM_001012709	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249558	71249558	+	Missense_Mutation	SNP	T	T	A	rs374587723		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:71249558T>A	ENST00000398534.3	+	1	488	c.457T>A	c.(457-459)Tgc>Agc	p.C153S		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	153	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TAAGCCCTGCTGCTGCTCTTC	0.602																																																	0													176.0	180.0	178.0					11																	71249558		2200	4294	6494	SO:0001583	missense	57830			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.457T>A	11.37:g.71249558T>A	ENSP00000420723:p.Cys153Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	12.36	1.913624	0.33815	.	.	ENSG00000241233	ENST00000398534	T	0.01767	4.65	1.63	0.358	0.16084	.	.	.	.	.	T	0.04003	0.0112	M	0.90252	3.1	0.24313	N	0.995073	B	0.02656	0.0	B	0.06405	0.002	T	0.27434	-1.0074	9	0.52906	T	0.07	.	4.9425	0.13973	0.2691:0.0:0.0:0.7308	.	153	O75690	KRA58_HUMAN	S	153	ENSP00000420723:C153S	ENSP00000420723:C153S	C	+	1	0	KRTAP5-8	70927206	0.006000	0.16342	0.812000	0.32479	0.182000	0.23217	0.150000	0.16263	0.076000	0.16826	0.459000	0.35465	TGC		0.602	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1		NM_021046	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637																																																	1	Substitution - Missense(1)	skin(1)											59.0	53.0	55.0					17																	39383027		2203	4300	6503	SO:0001583	missense	83899			AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.121G>T	17.37:g.39383027G>T	ENSP00000366950:p.Ala41Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC		0.637	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1			
LILRA6	79168	hgsc.bcm.edu	37	19	54745508	54745508	+	Missense_Mutation	SNP	G	G	A	rs61734497	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:54745508G>A	ENST00000396365.2	-	4	641	c.602C>T	c.(601-603)aCa>aTa	p.T201I	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.T201I|LILRA6_ENST00000270464.5_Missense_Mutation_p.T201I|LILRA6_ENST00000440558.2_Missense_Mutation_p.T201I|LILRA6_ENST00000419410.2_Missense_Mutation_p.T201I|LILRA6_ENST00000391735.3_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	201					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGGGTGTTTGTATAATAGTA	0.617													.|||	2021	0.403554	0.3759	0.415	5008	,	,		18511	0.5675		0.3628	False		,,,				2504	0.3057																0													39.0	44.0	42.0					19																	54745508		1868	3761	5629	SO:0001583	missense	79168			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.602C>T	19.37:g.54745508G>A	ENSP00000379651:p.Thr201Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	14.67	2.605213	0.46423	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55	2.38	-4.75	0.03239	Immunoglobulin-like fold (1);	2.023030	0.02301	N	0.071197	T	0.19485	0.0468	L	0.32530	0.975	0.80722	P	0.0	B;D;B;B;P	0.54207	0.17;0.965;0.16;0.077;0.671	B;P;B;B;B	0.58780	0.086;0.845;0.12;0.118;0.343	T	0.32719	-0.9896	9	0.66056	D	0.02	.	5.4334	0.16466	0.0:0.1945:0.454:0.3514	.	201;201;201;201;201	C9JFH3;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;LIRA6_HUMAN;.;.;.	I	201	ENSP00000390120:T201I;ENSP00000270464:T201I;ENSP00000411227:T201I;ENSP00000379651:T201I;ENSP00000245621:T201I	ENSP00000245621:T201I	T	-	2	0	LILRA6	59437320	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.356000	0.01087	-1.704000	0.01407	-2.001000	0.00444	ACA		0.617	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1		NM_024318	
LAIR1	3903	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	54872809	54872809	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:54872809C>T	ENST00000391742.2	-	3	230	c.78G>A	c.(76-78)ctG>ctA	p.L26L	LAIR1_ENST00000463489.1_5'UTR|LAIR1_ENST00000348231.4_Silent_p.L26L|LAIR1_ENST00000313038.6_Silent_p.L19L|LAIR1_ENST00000474878.1_Silent_p.L25L|LAIR1_ENST00000391743.3_Silent_p.L8L|LAIR1_ENST00000434277.2_Silent_p.L25L			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	26					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		AGGGTCTGGGCAGATCTTCTA	0.572																																																	0													99.0	104.0	103.0					19																	54872809		2203	4300	6503	SO:0001819	synonymous_variant	3903			AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6477	protein-coding gene	gene with protein product		602992	"""leukocyte-associated Ig-like receptor 1"""			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.78G>A	19.37:g.54872809C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000391742.2	37	CCDS12891.1																																																																																				0.572	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1			
MGAM2	93432	broad.mit.edu	37	7	141895981	141895982	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:141895981_141895982insG	ENST00000477922.3	+	38	4428_4429	c.4374_4375insG	c.(4375-4377)gggfs	p.G1459fs																	endometrium(1)|lung(5)	6						CAGGACAGCGAGGGGTCATCAT	0.535																																																	0																																										SO:0001589	frameshift_variant	100124692																														ENST00000477922.3:c.4378dupG	7.37:g.141895985_141895985dupG	ENSP00000420449:p.Gly1459fs	Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000477922.3	37																																																																																					0.535	RP11-1220K2.2-003	PUTATIVE	not_best_in_genome_evidence|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000351325.3			
RP11-252A24.2	0	broad.mit.edu	37	16	74372644	74372644	+	RNA	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:74372644A>G	ENST00000429810.2	-	0	1552																											TACCCTTGTCAGGGGGAACAA	0.443																																																	0																																												283922																															16.37:g.74372644A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000429810.2	37																																																																																					0.443	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			
TPTE2P6	374491	broad.mit.edu	37	13	25161438	25161438	+	RNA	SNP	T	T	A	rs3869320		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr13:25161438T>A	ENST00000453498.1	+	0	962				TPTE2P6_ENST00000440905.1_RNA																							CTCTTTATAATAAGATTCATT	0.378																																																	0																																												0																															13.37:g.25161438T>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000453498.1	37																																																																																					0.378	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			
LRRC46	90506	broad.mit.edu;hgsc.bcm.edu	37	17	45914323	45914323	+	Missense_Mutation	SNP	C	C	T	rs534847251		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:45914323C>T	ENST00000269025.4	+	8	1166	c.803C>T	c.(802-804)cCc>cTc	p.P268L		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	268										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GTCTCCTCACCCCAGGCCTCC	0.657													C|||	1	0.000199681	0.0	0.0	5008	,	,		17224	0.0		0.0	False		,,,				2504	0.001																0													84.0	90.0	88.0					17																	45914323		2203	4300	6503	SO:0001583	missense	90506				CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.803C>T	17.37:g.45914323C>T	ENSP00000269025:p.Pro268Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	37	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.274624	0.40194	.	.	ENSG00000141294	ENST00000269025	T	0.79141	-1.24	5.66	1.2	0.21068	.	0.658399	0.14103	N	0.341263	T	0.69124	0.3076	L	0.60455	1.87	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.62220	-0.6900	10	0.66056	D	0.02	-0.8363	4.8214	0.13392	0.0:0.5828:0.1568:0.2604	.	268;268	A8K9Q0;Q96FV0	.;LRC46_HUMAN	L	268	ENSP00000269025:P268L	ENSP00000269025:P268L	P	+	2	0	LRRC46	43269322	0.005000	0.15991	0.001000	0.08648	0.171000	0.22731	2.171000	0.42453	0.773000	0.33404	-0.147000	0.13772	CCC		0.657	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1		NM_033413	
LUZP2	338645	broad.mit.edu	37	11	25100121	25100121	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:25100121T>G	ENST00000336930.6	+	12	1024	c.958T>G	c.(958-960)Tct>Gct	p.S320A	LUZP2_ENST00000533227.1_Missense_Mutation_p.S234A			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	320						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GCCTCCTTGCTCTGAATGTGA	0.333																																																	0													77.0	82.0	80.0					11																	25100121		2203	4300	6503	SO:0001583	missense	338645			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.958T>G	11.37:g.25100121T>G	ENSP00000336817:p.Ser320Ala	Somatic		WXS	Illumina GAIIx	Phase_I	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071644	0.36566	.	.	ENSG00000187398	ENST00000336930;ENST00000533227	T;T	0.44482	0.93;0.92	5.35	-0.73	0.11154	.	0.572428	0.17377	N	0.176439	T	0.19685	0.0473	N	0.14661	0.345	0.22292	N	0.999229	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.14309	-1.0477	10	0.25106	T	0.35	-4.6723	5.2814	0.15678	0.4198:0.0:0.1143:0.4659	.	234;320	E9PN53;Q86TE4	.;LUZP2_HUMAN	A	320;234	ENSP00000336817:S320A;ENSP00000432952:S234A	ENSP00000336817:S320A	S	+	1	0	LUZP2	25056697	0.862000	0.29867	0.999000	0.59377	0.989000	0.77384	-0.229000	0.09098	0.077000	0.16863	0.482000	0.46254	TCT		0.333	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1		NM_001009909	
MADCAM1	8174	broad.mit.edu	37	19	501762	501762	+	Missense_Mutation	SNP	A	A	C	rs200007467		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:501762A>C	ENST00000215637.3	+	4	807	c.761A>C	c.(760-762)cAg>cCg	p.Q254P	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.Q35P|MADCAM1_ENST00000382683.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	254	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			Q -> P (in Ref. 1; AAC13661). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)	p.Q254P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCAGGAGCCTCCC	0.721																																																	1	Substitution - Missense(1)	kidney(1)											31.0	36.0	34.0					19																	501762		2194	4290	6484	SO:0001583	missense	8174			U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.761A>C	19.37:g.501762A>C	ENSP00000215637:p.Gln254Pro	Somatic		WXS	Illumina GAIIx	Phase_I	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	N	5.739	0.320845	0.10845	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09073	3.02	2.86	-5.72	0.02406	.	.	.	.	.	T	0.01940	0.0061	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	9	0.02654	T	1	.	3.6031	0.08032	0.3032:0.5048:0.0:0.192	.	254	Q13477	MADCA_HUMAN	P	278;270;262;254	ENSP00000215637:Q254P	ENSP00000215637:Q254P	Q	+	2	0	MADCAM1	452762	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.356000	0.00247	-1.159000	0.02807	-1.988000	0.00451	CAG		0.721	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1		NM_130760	
MADCAM1	8174	hgsc.bcm.edu	37	19	501767	501767	+	Missense_Mutation	SNP	C	C	T	rs78245161		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:501767C>T	ENST00000215637.3	+	4	812	c.766C>T	c.(766-768)Cct>Tct	p.P256S	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P37S|MADCAM1_ENST00000382683.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	256	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCCAGGAGCCTCCCGACAC	0.726																																																	0													31.0	35.0	33.0					19																	501767		2194	4286	6480	SO:0001583	missense	8174			U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.766C>T	19.37:g.501767C>T	ENSP00000215637:p.Pro256Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	c	5.207	0.223693	0.09863	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09538	2.97	2.86	2.86	0.33363	.	.	.	.	.	T	0.06188	0.0160	N	0.12182	0.205	0.54753	D	0.999986	D	0.63046	0.992	P	0.45577	0.486	T	0.38045	-0.9679	9	0.08837	T	0.75	.	9.9622	0.41704	0.0:1.0:0.0:0.0	.	256	Q13477	MADCA_HUMAN	S	280;272;264;256	ENSP00000215637:P256S	ENSP00000215637:P256S	P	+	1	0	MADCAM1	452767	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	-0.228000	0.09114	1.548000	0.49413	0.638000	0.83543	CCT		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1		NM_130760	
MAP2K3	5606	hgsc.bcm.edu	37	17	21204187	21204187	+	Splice_Site	SNP	G	G	T	rs56067280	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:21204187G>T	ENST00000342679.4	+	5	530	c.281G>T	c.(280-282)cGg>cTg	p.R94L	MAP2K3_ENST00000316920.6_Splice_Site_p.R65L|MAP2K3_ENST00000361818.5_Splice_Site_p.R65L	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	94	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> L (in dbSNP:rs56067280). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R98L(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TCCCTGCAGCGGATCCGGGCC	0.607																																																	1	Substitution - Missense(1)	large_intestine(1)																																								SO:0001630	splice_region_variant	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.280-1G>T	17.37:g.21204187G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	1092	0.5	246	0.5	181	0.5	286	0.5	379	0.5	G	17.14	3.314111	0.60414	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;D	0.89123	1.09;1.09;-2.47	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	N	0.20610	0.595	0.09310	P	0.9999999857583	D	0.58268	0.982	P	0.51487	0.671	T	0.29458	-1.0011	9	0.72032	D	0.01	-28.208	18.4815	0.90813	0.0:0.0:1.0:0.0	rs56067280	94	P46734	MP2K3_HUMAN	L	94;65;65;65;98	ENSP00000345083:R94L;ENSP00000355081:R65L;ENSP00000434068:R65L	ENSP00000319139:R98L	R	+	2	0	MAP2K3	21144780	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	7.845000	0.86875	2.359000	0.80004	0.655000	0.94253	CGG		0.607	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2		NM_145109	Missense_Mutation
MAP2K3	5606	hgsc.bcm.edu	37	17	21204192	21204192	+	Missense_Mutation	SNP	C	C	T	rs56216806	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:21204192C>T	ENST00000342679.4	+	5	535	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W	MAP2K3_ENST00000316920.6_Missense_Mutation_p.R67W|MAP2K3_ENST00000361818.5_Missense_Mutation_p.R67W	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> W (in dbSNP:rs56216806). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GCAGCGGATCCGGGCCACCGT	0.622																																																	0																																										SO:0001583	missense	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.286C>T	17.37:g.21204192C>T	ENSP00000345083:p.Arg96Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	1092	0.5	246	0.5	181	0.5	286	0.5	379	0.5	C	14.98	2.698443	0.48307	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;T	0.66815	-0.23;-0.23;-0.23	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	M	0.77486	2.375	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.42565	-0.9444	10	0.72032	D	0.01	-27.0478	13.4514	0.61174	0.1566:0.8434:0.0:0.0	rs56216806	96	P46734	MP2K3_HUMAN	W	96;67;67;67;100	ENSP00000345083:R96W;ENSP00000355081:R67W;ENSP00000434068:R67W	ENSP00000319139:R100W	R	+	1	2	MAP2K3	21144785	0.986000	0.35501	1.000000	0.80357	0.876000	0.50452	2.458000	0.45014	2.359000	0.80004	0.655000	0.94253	CGG		0.622	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2		NM_145109	
MUC17	140453	hgsc.bcm.edu	37	7	100684091	100684092	+	Frame_Shift_Ins	INS	-	-	C	rs368858885		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:100684091_100684092insC	ENST00000306151.4	+	3	9458_9459	c.9394_9395insC	c.(9394-9396)accfs	p.T3132fs		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3132	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCTGTTGACACCAGCACACCT	0.49																																																	0																																										SO:0001589	frameshift_variant	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9396dupC	7.37:g.100684093_100684093dupC	ENSP00000302716:p.Thr3132fs	Somatic		WXS	Illumina HiSeq	Phase_I	O14761|Q685J2|Q8TDH7	Frame_Shift_Ins	INS	ENST00000306151.4	37	CCDS34711.1																																																																																				0.490	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1		NM_001040105	
MUC2	4583	hgsc.bcm.edu	37	11	1093135	1093135	+	Missense_Mutation	SNP	A	A	C	rs56080332		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1093135A>C	ENST00000441003.2	+	30	4981	c.4954A>C	c.(4954-4956)Acg>Ccg	p.T1652P	MUC2_ENST00000359061.5_Missense_Mutation_p.T1619P|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaaccacgacacccat	0.627																																																	0													104.0	167.0	145.0					11																	1093135		1799	3362	5161	SO:0001583	missense	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4954A>C	11.37:g.1093135A>C	ENSP00000415183:p.Thr1652Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	1.105	-0.659880	0.03454	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08370	3.1;3.14	1.75	-3.51	0.04696	.	7739.210000	0.00166	N	0.000003	T	0.05914	0.0154	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34304	-0.9834	9	0.46703	T	0.11	.	3.4472	0.07484	0.5097:0.3224:0.0:0.1679	rs56080332	1652	E7EUV1	.	P	1652;1619	ENSP00000415183:T1652P;ENSP00000351956:T1619P	ENSP00000351956:T1619P	T	+	1	0	MUC2	1083135	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.830000	0.00744	-1.075000	0.03129	-1.890000	0.00535	ACG		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2		NM_002457	
MUC4	4585	hgsc.bcm.edu	37	3	195510030	195510030	+	Silent	SNP	C	C	G	rs374297426	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr3:195510030C>G	ENST00000463781.3	-	2	8880	c.8421G>C	c.(8419-8421)tcG>tcC	p.S2807S	MUC4_ENST00000475231.1_Silent_p.S2807S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S2807S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGACACTGACGAAGCGTCGG	0.582													.|||	29	0.00579073	0.0174	0.0014	5008	,	,		6131	0.002		0.001	False		,,,				2504	0.002																1	Substitution - coding silent(1)	endometrium(1)											75.0	46.0	55.0					3																	195510030		683	1492	2175	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8421G>C	3.37:g.195510030C>G		Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC6	4588	hgsc.bcm.edu	37	11	1017074	1017074	+	Silent	SNP	A	A	G	rs79277162		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1017074A>G	ENST00000421673.2	-	31	5777	c.5727T>C	c.(5725-5727)ttT>ttC	p.F1909F		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1909	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGCCGTGCTAAATGAGCTTG	0.552																																																	0													687.0	705.0	699.0					11																	1017074		2198	4284	6482	SO:0001819	synonymous_variant	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5727T>C	11.37:g.1017074A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																				0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MUC6	4588	hgsc.bcm.edu	37	11	1018048	1018048	+	Missense_Mutation	SNP	A	A	G	rs12787400		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1018048A>G	ENST00000421673.2	-	31	4803	c.4753T>C	c.(4753-4755)Ttc>Ctc	p.F1585L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1585	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGAAGAGAAGGGACTGCTC	0.592																																																	0													262.0	264.0	264.0					11																	1018048		2164	4250	6414	SO:0001583	missense	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4753T>C	11.37:g.1018048A>G	ENSP00000406861:p.Phe1585Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	a	0.021	-1.421658	0.01126	.	.	ENSG00000184956	ENST00000421673	T	0.17054	2.3	1.55	-0.407	0.12385	.	.	.	.	.	T	0.08846	0.0219	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.19946	0.027	T	0.42120	-0.9470	9	0.10902	T	0.67	.	1.9807	0.03426	0.2646:0.3934:0.0:0.3421	.	1585	Q6W4X9	MUC6_HUMAN	L	1585	ENSP00000406861:F1585L	ENSP00000406861:F1585L	F	-	1	0	MUC6	1008048	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.590000	0.00211	-0.114000	0.11936	-2.307000	0.00257	TTC		0.592	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MUC6	4588	hgsc.bcm.edu	37	11	1018059	1018059	+	Missense_Mutation	SNP	C	C	T	rs78336072		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1018059C>T	ENST00000421673.2	-	31	4792	c.4742G>A	c.(4741-4743)gGg>gAg	p.G1581E		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1581	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGACTGCTCCCTGTAGGTGG	0.587																																																	0													260.0	264.0	262.0					11																	1018059		2165	4256	6421	SO:0001583	missense	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4742G>A	11.37:g.1018059C>T	ENSP00000406861:p.Gly1581Glu	Somatic		WXS	Illumina HiSeq	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	0.082	-1.181258	0.01633	.	.	ENSG00000184956	ENST00000421673	T	0.17854	2.25	1.66	-3.31	0.04988	.	.	.	.	.	T	0.09379	0.0231	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30297	-0.9983	9	0.23302	T	0.38	.	0.8326	0.01133	0.3082:0.154:0.1158:0.422	.	1581	Q6W4X9	MUC6_HUMAN	E	1581	ENSP00000406861:G1581E	ENSP00000406861:G1581E	G	-	2	0	MUC6	1008059	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.459000	0.02370	-3.040000	0.00263	-0.742000	0.03525	GGG		0.587	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MUC6	4588	hgsc.bcm.edu	37	11	1018382	1018382	+	Silent	SNP	A	A	G	rs76138285	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:1018382A>G	ENST00000421673.2	-	31	4469	c.4419T>C	c.(4417-4419)tcT>tcC	p.S1473S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1473	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTTGGAGGCAGATGTGGCCA	0.577													a|||	6	0.00119808	0.0038	0.0014	5008	,	,		21041	0.0		0.0	False		,,,				2504	0.0																0													216.0	212.0	213.0					11																	1018382		2180	4273	6453	SO:0001819	synonymous_variant	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4419T>C	11.37:g.1018382A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																				0.577	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MYLK3	91807	broad.mit.edu;hgsc.bcm.edu	37	16	46766320	46766320	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:46766320C>G	ENST00000394809.4	-	4	1377	c.1262G>C	c.(1261-1263)gGg>gCg	p.G421A	MYLK3_ENST00000536476.1_Missense_Mutation_p.G80A	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	421					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AGGCTCGGCCCCAGCCCTTTG	0.677																																																	0													69.0	79.0	76.0					16																	46766320		2203	4300	6503	SO:0001583	missense	91807			AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1262G>C	16.37:g.46766320C>G	ENSP00000378288:p.Gly421Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	6.233	0.411116	0.11812	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.69175	-0.38;-0.29	5.1	0.218	0.15270	.	0.256775	0.20554	N	0.090053	T	0.42562	0.1208	L	0.32530	0.975	0.09310	N	1	B;B	0.34372	0.278;0.451	B;B	0.30179	0.057;0.112	T	0.21518	-1.0243	10	0.12430	T	0.62	.	3.9708	0.09452	0.0:0.356:0.3934:0.2506	.	421;421	B5BUL9;Q32MK0	.;MYLK3_HUMAN	A	421;80	ENSP00000378288:G421A;ENSP00000439297:G80A	ENSP00000378288:G421A	G	-	2	0	MYLK3	45323821	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-0.842000	0.04354	0.155000	0.19261	-0.258000	0.10820	GGG		0.677	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2		NM_182493	
N4BP2	55728	broad.mit.edu	37	4	40121716	40121716	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr4:40121716delG	ENST00000261435.6	+	9	2401	c.1985delG	c.(1984-1986)agafs	p.R662fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	662					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AACAAAAGAAGAAAAGAAATA	0.338																																																	0													57.0	66.0	63.0					4																	40121716		2202	4298	6500	SO:0001589	frameshift_variant	55728			AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.1985delG	4.37:g.40121716delG	ENSP00000261435:p.Arg662fs	Somatic		WXS	Illumina GAIIx	Phase_I	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	37	CCDS3457.1																																																																																				0.338	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2		NM_018177	
NBPF10	100132406	broad.mit.edu	37	1	145301802	145301802	+	Silent	SNP	C	C	G	rs6690575	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:145301802C>G	ENST00000369339.3	+	4	511	c.258C>G	c.(256-258)ctC>ctG	p.L86L	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Silent_p.L86L|NBPF10_ENST00000342960.5_Silent_p.L357L			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	357						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L86L(1)|p.L357L(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CAGAGCAGCTCAAGCAAGCTG	0.522																																																	2	Substitution - coding silent(2)	NS(2)																																								SO:0001819	synonymous_variant	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.258C>G	1.37:g.145301802C>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000369339.3	37																																																																																					0.522	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3		NM_001039703	
NLRP5	126206	broad.mit.edu;ucsc.edu	37	19	56515289	56515289	+	Silent	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:56515289A>G	ENST00000390649.3	+	2	270	c.270A>G	c.(268-270)gaA>gaG	p.E90E		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	90	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AATCTTCAGAATCGACCACAT	0.458																																																	0													90.0	87.0	88.0					19																	56515289		1945	4151	6096	SO:0001819	synonymous_variant	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.270A>G	19.37:g.56515289A>G		Somatic		WXS	Illumina GAIIx	Phase_I	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																				0.458	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1		NM_153447	
OR10A5	144124	broad.mit.edu	37	11	6867462	6867462	+	Silent	SNP	G	G	A	rs543931840		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:6867462G>A	ENST00000299454.4	+	1	580	c.549G>A	c.(547-549)ccG>ccA	p.P183P	OR10A5_ENST00000379831.2_Silent_p.P187P			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	183					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P183P(2)		endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTGACAGCCCGCCTGTGCTGA	0.527													A|||	1	0.000199681	0.0	0.0	5008	,	,		23000	0.001		0.0	False		,,,				2504	0.0				Pancreas(44;21 1072 25662 28041 45559)												2	Substitution - coding silent(2)	kidney(2)											180.0	152.0	161.0					11																	6867462		2201	4296	6497	SO:0001819	synonymous_variant	144124			AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.549G>A	11.37:g.6867462G>A		Somatic		WXS	Illumina GAIIx	Phase_I	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																				0.527	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1		NM_178168	
OR2T12	127064	hgsc.bcm.edu	37	1	248458717	248458717	+	Missense_Mutation	SNP	C	C	G	rs12745228	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:248458717C>G	ENST00000317996.1	-	1	163	c.164G>C	c.(163-165)aGg>aCg	p.R55T		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			GTACATGGGCCTGTGGAGCCG	0.527																																																	0													81.0	64.0	70.0					1																	248458717		2203	4298	6501	SO:0001583	missense	127064			BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.164G>C	1.37:g.248458717C>G	ENSP00000324583:p.Arg55Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	0.014	-1.591375	0.00864	.	.	ENSG00000177201	ENST00000317996	T	0.00342	8.03	1.55	0.445	0.16597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36303	N	0.002679	T	0.00039	0.0001	N	0.00020	-2.765	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46386	-0.9195	9	0.02654	T	1	.	9.5701	0.39422	0.0:0.4144:0.5856:0.0	rs12745228	55	Q8NG77	O2T12_HUMAN	T	55	ENSP00000324583:R55T	ENSP00000324583:R55T	R	-	2	0	OR2T12	246525340	0.000000	0.05858	0.130000	0.21974	0.176000	0.22953	0.396000	0.20867	-1.867000	0.01144	-1.614000	0.00798	AGG		0.527	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1		NM_001004692	
OTX1	5013	broad.mit.edu;hgsc.bcm.edu	37	2	63283088	63283088	+	Silent	SNP	C	C	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:63283088C>A	ENST00000282549.2	+	5	978	c.702C>A	c.(700-702)ggC>ggA	p.G234G	OTX1_ENST00000366671.3_Silent_p.G234G	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	234					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					ACGGCCAAGGCTACCCTACGC	0.647																																																	0													62.0	60.0	60.0					2																	63283088		2203	4300	6503	SO:0001819	synonymous_variant	5013				CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"""Homeoboxes / PRD class"""	8521	protein-coding gene	gene with protein product		600036	"""orthodenticle (Drosophila) homolog 1"", ""orthodenticle homolog 1 (Drosophila)"""			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.702C>A	2.37:g.63283088C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NHA2|B3KTJ4|Q53TG6	Silent	SNP	ENST00000282549.2	37	CCDS1873.1																																																																																				0.647	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			
PABPC1	26986	hgsc.bcm.edu	37	8	101730036	101730037	+	Frame_Shift_Ins	INS	-	-	C	rs545344384	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr8:101730036_101730037insC	ENST00000318607.5	-	3	1595_1596	c.467_468insG	c.(466-468)gaafs	p.E156fs	PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.E111fs|PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.E124fs|PABPC1_ENST00000519596.1_5'Flank	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	156	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)			CATTCATTTTTTCAATAGCTCT	0.337													-|-|C|insertion	726	0.144968	0.2133	0.1124	5008	,	,		20837	0.0764		0.0825	False		,,,				2504	0.2106																0																																										SO:0001589	frameshift_variant	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.467_468insG	8.37:g.101730036_101730037insC	ENSP00000313007:p.Glu156fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q15097|Q93004	Frame_Shift_Ins	INS	ENST00000318607.5	37	CCDS6289.1																																																																																				0.337	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1		NM_002568	
PCMTD1	115294	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	52733037	52733037	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr8:52733037C>T	ENST00000360540.5	-	7	1354	c.948G>A	c.(946-948)gaG>gaA	p.E316E	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Silent_p.E240E|PCMTD1_ENST00000522514.1_Silent_p.E316E	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	316						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				GAtctttttcctcctcttctt	0.393																																																	0																																										SO:0001819	synonymous_variant	115294				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.948G>A	8.37:g.52733037C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q96FK9	Silent	SNP	ENST00000360540.5	37	CCDS6148.1																																																																																				0.393	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2		NM_052937	
PDPR	55066	hgsc.bcm.edu	37	16	70154480	70154480	+	Missense_Mutation	SNP	A	A	G	rs587776506|rs200469748	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:70154480A>G	ENST00000288050.4	+	3	1042	c.85A>G	c.(85-87)Acg>Gcg	p.T29A	PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Missense_Mutation_p.T29A	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	29				T -> A (in Ref. 3; CAH10555). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)	p.T29A(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		AAGAAACAGCACGTCAGCTGC	0.572																																																	1	Substitution - Missense(1)	central_nervous_system(1)											51.0	53.0	52.0					16																	70154480		2117	4237	6354	SO:0001583	missense	55066				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.85A>G	16.37:g.70154480A>G	ENSP00000288050:p.Thr29Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	G	1.592	-0.528814	0.04112	.	.	ENSG00000090857	ENST00000288050	T	0.69435	-0.4	4.13	-5.16	0.02857	.	1.037440	0.07658	N	0.933150	T	0.37320	0.0999	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	10	0.06494	T	0.89	.	5.1635	0.15073	0.443:0.0:0.2448:0.3121	.	29	Q8NCN5	PDPR_HUMAN	A	29	ENSP00000288050:T29A	ENSP00000288050:T29A	T	+	1	0	PDPR	68711981	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.944000	0.03913	-0.959000	0.03618	-0.318000	0.08688	ACG		0.572	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1		NM_017990	
PER2	8864	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	239186456	239186456	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:239186456T>C	ENST00000254657.3	-	2	401	c.122A>G	c.(121-123)cAt>cGt	p.H41R	PER2_ENST00000440245.1_Missense_Mutation_p.H41R|PER2_ENST00000254658.3_Missense_Mutation_p.H41R|PER2_ENST00000355768.2_Missense_Mutation_p.H41R	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	41					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		GTTGGTCTCATGTCCACTGGA	0.652																																																	0													69.0	66.0	67.0					2																	239186456		2203	4300	6503	SO:0001583	missense	8864			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.122A>G	2.37:g.239186456T>C	ENSP00000254657:p.His41Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	T	8.143	0.785554	0.16189	.	.	ENSG00000132326	ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768;ENST00000431832	T;T;T;T;T	0.42513	2.93;1.0;2.03;1.0;0.97	4.68	4.68	0.58851	.	0.364872	0.30374	N	0.009768	T	0.23846	0.0577	N	0.08118	0	0.21064	N	0.999792	B;B;P;B	0.35226	0.152;0.033;0.491;0.058	B;B;B;B	0.32465	0.08;0.01;0.146;0.03	T	0.24440	-1.0160	10	0.87932	D	0	-19.4281	12.4123	0.55473	0.0:0.0:0.0:1.0	.	41;41;41;41	F5GYD5;B4DH14;O15055-2;O15055	.;.;.;PER2_HUMAN	R	41	ENSP00000254657:H41R;ENSP00000254658:H41R;ENSP00000397516:H41R;ENSP00000348013:H41R;ENSP00000405891:H41R	ENSP00000254657:H41R	H	-	2	0	PER2	238851195	0.912000	0.30974	0.170000	0.22879	0.047000	0.14425	2.195000	0.42677	1.881000	0.54492	0.460000	0.39030	CAT		0.652	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1		NM_022817	
PLA2G4B	100137049	broad.mit.edu;hgsc.bcm.edu	37	15	42132809	42132809	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:42132809G>C	ENST00000452633.1	+	4	522	c.170G>C	c.(169-171)aGc>aCc	p.S57T	PLA2G4B_ENST00000458483.1_Missense_Mutation_p.S57T|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.S288T|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.S288T|PLA2G4B_ENST00000542534.2_Missense_Mutation_p.S288T			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	57	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		AACAGCAGTAGCCCTGTCTGG	0.617																																																	0													76.0	78.0	78.0					15																	42132809		2203	4300	6503	SO:0001583	missense	100137049			AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.170G>C	15.37:g.42132809G>C	ENSP00000396045:p.Ser57Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	.	.	.	.	.	.	.	.	.	.	.	15.34	2.805255	0.50315	.	.	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.04	0.346	0.16017	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.428514	0.25575	N	0.029723	T	0.47930	0.1472	N	0.17248	0.465	0.21984	N	0.999439	B;B;B	0.32753	0.383;0.065;0.287	B;B;B	0.34590	0.186;0.037;0.085	T	0.47812	-0.9088	10	0.87932	D	0	-1.8224	9.8622	0.41120	0.8494:0.0:0.1506:0.0	.	57;288;288	P0C869;P0C869-7;P0C869-6	PA24B_HUMAN;.;.	T	288;288;57;57	ENSP00000371886:S288T;ENSP00000342785:S288T;ENSP00000416610:S57T;ENSP00000396045:S57T	ENSP00000342785:S288T	S	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39920101	0.128000	0.22383	0.987000	0.45799	0.951000	0.60555	1.059000	0.30517	0.196000	0.20367	-0.136000	0.14681	AGC		0.617	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1		NM_001114633	
PLCH1	23007	broad.mit.edu;ucsc.edu	37	3	155199834	155199834	+	Silent	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr3:155199834A>G	ENST00000340059.7	-	23	4004	c.4005T>C	c.(4003-4005)tcT>tcC	p.S1335S	PLCH1_ENST00000460012.1_Silent_p.S1297S|PLCH1_ENST00000334686.6_Silent_p.S1297S|PLCH1_ENST00000414191.1_Silent_p.S1297S|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000494598.1_Intron	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1335					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AATCAGGGGAAGAGGCAGGGC	0.498																																																	0													54.0	58.0	57.0					3																	155199834		2203	4300	6503	SO:0001819	synonymous_variant	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.4005T>C	3.37:g.155199834A>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	37	CCDS46939.1																																																																																				0.498	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1		NM_014996	
KIZ-AS1	101929591	broad.mit.edu	37	20	21143767	21143767	+	RNA	DEL	A	A	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr20:21143767delA	ENST00000591761.1	-	0	5051				PLK1S1_ENST00000457464.1_RNA|RP5-872K7.7_ENST00000425746.2_RNA																							CCTGATTCAGAAAAGGAATCC	0.368																																																	0													98.0	96.0	96.0					20																	21143767		1839	4098	5937			55857																															20.37:g.21143767delA		Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Del	DEL	ENST00000591761.1	37																																																																																					0.368	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			
PRB1	5542	hgsc.bcm.edu	37	12	11506464	11506464	+	Intron	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:11506464C>T	ENST00000500254.2	-	4	351				PRB1_ENST00000545626.1_Intron|PRB1_ENST00000546254.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GTGGGGGACCCTGAGGTTTCT	0.607																																																	0													8.0	5.0	6.0					12																	11506464		1009	1687	2696	SO:0001627	intron_variant	5542				CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.314-140G>A	12.37:g.11506464C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Silent	SNP	ENST00000500254.2	37	CCDS8642.1																																																																																				0.607	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1		NM_005039	
PRG4	10216	hgsc.bcm.edu	37	1	186276624	186276624	+	Silent	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:186276624A>G	ENST00000445192.2	+	7	1818	c.1773A>G	c.(1771-1773)gaA>gaG	p.E591E	PRG4_ENST00000367485.4_Silent_p.E498E|PRG4_ENST00000367483.4_Silent_p.E550E|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.E548E	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	591	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTCCCAAGGAACCTGCACCCA	0.642																																																	0													94.0	89.0	91.0					1																	186276624		2203	4300	6503	SO:0001819	synonymous_variant	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1773A>G	1.37:g.186276624A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																				0.642	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1		NM_005807	
PRR21	643905	hgsc.bcm.edu	37	2	240982219	240982219	+	Missense_Mutation	SNP	A	A	G	rs74006013		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:240982219A>G	ENST00000408934.1	-	1	180	c.181T>C	c.(181-183)Tcc>Ccc	p.S61P		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	61	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						AGAGCCGTGGATGAAGGGCCG	0.607																																																	0													130.0	115.0	120.0					2																	240982219		2203	4300	6503	SO:0001583	missense	643905			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.181T>C	2.37:g.240982219A>G	ENSP00000386166:p.Ser61Pro	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	6.168	0.399216	0.11696	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.26223	1.75;1.75	1.5	-2.16	0.07080	.	.	.	.	.	T	0.10637	0.0260	N	0.08118	0	0.09310	N	1	B	0.15719	0.014	B	0.17722	0.019	T	0.25293	-1.0136	9	0.54805	T	0.06	.	2.7666	0.05322	0.3479:0.0:0.4377:0.2145	.	61	Q8WXC7	PRR21_HUMAN	P	61	ENSP00000386166:S61P;ENSP00000418240:S61P	ENSP00000386166:S61P	S	-	1	0	PRR21	240630892	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.540000	0.00437	-0.607000	0.05738	-0.484000	0.04775	TCC		0.607	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001080835	
PTCD1	26024	broad.mit.edu;hgsc.bcm.edu	37	7	99022964	99022964	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:99022964C>T	ENST00000292478.4	-	6	1441	c.1191G>A	c.(1189-1191)ggG>ggA	p.G397G	PTCD1_ENST00000555673.1_Silent_p.G446G|ATP5J2-PTCD1_ENST00000413834.1_Silent_p.G446G	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	397					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)			GCTCTGGAGGCCCAAGTGCCT	0.642																																																	0													86.0	85.0	85.0					7																	99022964		2203	4300	6503	SO:0001819	synonymous_variant	26024			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.1191G>A	7.37:g.99022964C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																				0.642	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1		NM_015545	
PTPRS	5802	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	5214437	5214437	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:5214437G>A	ENST00000587303.1	-	29	4648	c.4549C>T	c.(4549-4551)Cag>Tag	p.Q1517*	PTPRS_ENST00000353284.2_Nonsense_Mutation_p.Q1070*|PTPRS_ENST00000357368.4_Nonsense_Mutation_p.Q1517*|PTPRS_ENST00000262963.6_Nonsense_Mutation_p.Q1497*|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000372412.4_Nonsense_Mutation_p.Q1518*|PTPRS_ENST00000588012.1_Nonsense_Mutation_p.Q1479*|PTPRS_ENST00000592099.1_Nonsense_Mutation_p.Q1070*|PTPRS_ENST00000348075.2_Nonsense_Mutation_p.Q1479*			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1517	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	AACGTGACCTGGATGAAGCCG	0.587																																																	0													135.0	101.0	113.0					19																	5214437		2203	4300	6503	SO:0001587	stop_gained	5802			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4549C>T	19.37:g.5214437G>A	ENSP00000467537:p.Gln1517*	Somatic		WXS	Illumina HiSeq	Phase_I	O75255|O75870|Q15718|Q16341|Q2M3R7	Nonsense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	G	43	10.141872	0.99345	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	.	.	.	3.12	3.12	0.35913	.	0.000000	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.721	0.69305	0.0:0.0:1.0:0.0	.	.	.	.	X	1112;1518;1517;1517;1508;1497;1479;1099;1074;1070	.	ENSP00000262963:Q1497X	Q	-	1	0	PTPRS	5165437	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	9.389000	0.97243	1.772000	0.52199	0.313000	0.20887	CAG		0.587	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			
RASGRP4	115727	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38904046	38904046	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:38904046A>T	ENST00000587738.1	-	10	1369	c.1299T>A	c.(1297-1299)tgT>tgA	p.C433*	RASGRP4_ENST00000587753.1_Nonsense_Mutation_p.C364*|RASGRP4_ENST00000293062.9_Nonsense_Mutation_p.C336*|RASGRP4_ENST00000433821.2_Nonsense_Mutation_p.C341*|RASGRP4_ENST00000586305.1_Nonsense_Mutation_p.C419*|RASGRP4_ENST00000426920.2_Nonsense_Mutation_p.C244*|RASGRP4_ENST00000454404.2_Nonsense_Mutation_p.C399*			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	433					activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGCTCTTGGGACAACGCGGCT	0.592																																																	0													27.0	35.0	32.0					19																	38904046		2038	4176	6214	SO:0001587	stop_gained	115727			AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"""EF-hand domain containing"""	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1299T>A	19.37:g.38904046A>T	ENSP00000465772:p.Cys433*	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Nonsense_Mutation	SNP	ENST00000587738.1	37	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	A	38	6.812340	0.97857	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	.	.	.	5.25	-0.452	0.12205	.	0.131736	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-4.3089	9.7573	0.40510	0.6134:0.0:0.3866:0.0	.	.	.	.	X	341;336;244;433;433	.	ENSP00000293062:C336X	C	-	3	2	RASGRP4	43595886	1.000000	0.71417	0.991000	0.47740	0.838000	0.47535	1.367000	0.34204	-0.091000	0.12440	0.533000	0.62120	TGT		0.592	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1		NM_170604	
RBM33	155435	broad.mit.edu	37	7	155473566	155473567	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr7:155473566_155473567delAG	ENST00000401878.3	+	5	729_730	c.531_532delAG	c.(529-534)ttagacfs	p.D178fs	RBM33_ENST00000287912.3_Frame_Shift_Del_p.D178fs|RBM33_ENST00000392759.3_Frame_Shift_Del_p.D178fs	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	178	Glu-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		ATGAAGTGTTAGACATCGAGAT	0.431																																																	0																																										SO:0001589	frameshift_variant	155435			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.531_532delAG	7.37:g.155473566_155473567delAG	ENSP00000384160:p.Asp178fs	Somatic		WXS	Illumina GAIIx	Phase_I	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	37	CCDS5941.2																																																																																				0.431	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3		NM_001008408	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448608	89448608	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:89448608G>A	ENST00000321792.5	-	2	1329	c.902C>T	c.(901-903)cCg>cTg	p.P301L	CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.P301L|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'Flank	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	301	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										ATAAGATGGCGGGGGCCCTCG	0.483																																																	0													172.0	172.0	172.0					1																	89448608		2203	4300	6503	SO:0001583	missense	494115			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.902C>T	1.37:g.89448608G>A	ENSP00000318415:p.Pro301Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022446	0.35701	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78126	-1.15;-1.15	1.41	0.0579	0.14325	.	0.060058	0.64402	D	0.000002	T	0.52629	0.1746	M	0.66939	2.045	0.46725	D	0.999174	B	0.34255	0.445	B	0.20577	0.03	T	0.56341	-0.7995	10	0.52906	T	0.07	-2.8526	6.2127	0.20638	0.0:0.0:0.7093:0.2907	.	301	Q96E39	RBMXL_HUMAN	L	301	ENSP00000318415:P301L;ENSP00000446099:P301L	ENSP00000318415:P301L	P	-	2	0	RBMXL1	89221196	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	6.229000	0.72294	0.760000	0.33108	0.306000	0.20318	CCG		0.483	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3		NM_019610	
RHOQ	23433	broad.mit.edu	37	2	46803262	46803262	+	Missense_Mutation	SNP	A	A	G	rs557488131		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:46803262A>G	ENST00000238738.4	+	3	557	c.238A>G	c.(238-240)Atg>Gtg	p.M80V	RP11-417F21.1_ENST00000506009.2_RNA|RHOQ_ENST00000465198.1_3'UTR	NM_012249.3	NP_036381.2	P17081	RHOQ_HUMAN	ras homolog family member Q	80					cellular response to insulin stimulus (GO:0032869)|cortical actin cytoskeleton organization (GO:0030866)|GTP catabolic process (GO:0006184)|insulin receptor signaling pathway (GO:0008286)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GBD domain binding (GO:0032427)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|profilin binding (GO:0005522)	p.M80V(1)		skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATCTTACCCAATGACCGATGT	0.393													A|||	1	0.000199681	0.0	0.0	5008	,	,		18452	0.0		0.001	False		,,,				2504	0.0																1	Substitution - Missense(1)	endometrium(1)											99.0	89.0	92.0					2																	46803262		2203	4300	6503	SO:0001583	missense	23433			M31470	CCDS33191.1	2p21	2012-02-27	2012-02-27	2004-03-24	ENSG00000119729	ENSG00000119729			17736	protein-coding gene	gene with protein product		605857	"""RAS-like, family 7, member A"", ""ras homolog gene family, member Q"""	RASL7A, ARHQ		2108320	Standard	NM_012249		Approved	TC10	uc002rva.3	P17081	OTTHUMG00000150653	ENST00000238738.4:c.238A>G	2.37:g.46803262A>G	ENSP00000238738:p.Met80Val	Somatic		WXS	Illumina GAIIx	Phase_I	D6W5A6|Q0VGN1|Q52LS8|Q53SJ1|Q6NS39|Q6P146|Q7Z480	Missense_Mutation	SNP	ENST00000238738.4	37	CCDS33191.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.367334	0.41902	.	.	ENSG00000119729	ENST00000238738;ENST00000482449	T;T	0.76186	-1.0;3.4	5.43	4.26	0.50523	Small GTP-binding protein domain (1);	0.034638	0.85682	D	0.000000	T	0.65637	0.2710	L	0.38175	1.15	0.58432	D	0.99999	B	0.15141	0.012	B	0.12156	0.007	T	0.63202	-0.6690	10	0.87932	D	0	.	12.6767	0.56897	0.862:0.1379:0.0:0.0	.	80	P17081	RHOQ_HUMAN	V	80;1	ENSP00000238738:M80V;ENSP00000428006:M1V	ENSP00000238738:M80V	M	+	1	0	RHOQ	46656766	1.000000	0.71417	0.993000	0.49108	0.882000	0.50991	7.317000	0.79018	1.055000	0.40461	-0.316000	0.08728	ATG		0.393	RHOQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319409.1		NM_012249	
RPH3A	22895	hgsc.bcm.edu	37	12	113314465	113314465	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:113314465C>T	ENST00000389385.4	+	13	1462	c.965C>T	c.(964-966)cCt>cTt	p.P322L	RPH3A_ENST00000420983.2_Missense_Mutation_p.P322L|RPH3A_ENST00000415485.3_Missense_Mutation_p.P322L|RPH3A_ENST00000548866.1_Missense_Mutation_p.P273L|RPH3A_ENST00000551052.1_Missense_Mutation_p.P318L|RPH3A_ENST00000543106.2_Missense_Mutation_p.P322L|RPH3A_ENST00000447659.2_Missense_Mutation_p.P273L|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	322	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CCGAGCGACCCTGGGACCACT	0.602																																																	0													30.0	26.0	27.0					12																	113314465		2198	4300	6498	SO:0001583	missense	22895			AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.965C>T	12.37:g.113314465C>T	ENSP00000374036:p.Pro322Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	6.729	0.503239	0.12822	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.62232	0.05;0.05;0.04;0.05;0.05;0.04;0.05	5.05	4.16	0.48862	.	0.302651	0.27754	N	0.017981	T	0.50154	0.1599	L	0.47716	1.5	0.09310	N	0.999992	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.002	T	0.32161	-0.9917	10	0.16420	T	0.52	.	9.3877	0.38354	0.0:0.8998:0.0:0.1002	.	273;322;322;318	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	L	322;322;273;318;322;273;322	ENSP00000440384:P322L;ENSP00000374036:P322L;ENSP00000413254:P273L;ENSP00000448297:P318L;ENSP00000405357:P322L;ENSP00000450347:P273L;ENSP00000408889:P322L	ENSP00000374036:P322L	P	+	2	0	RPH3A	111798848	0.002000	0.14202	0.024000	0.17045	0.074000	0.17049	1.560000	0.36331	1.109000	0.41680	0.511000	0.50034	CCT		0.602	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1		NM_014954	
RPS6KC1	26750	broad.mit.edu;ucsc.edu	37	1	213415458	213415458	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:213415458A>G	ENST00000366960.3	+	11	2789	c.2639A>G	c.(2638-2640)aAg>aGg	p.K880R	RPS6KC1_ENST00000543354.1_Missense_Mutation_p.K583R|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.K868R|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.K668R	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	880	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAAGGAGACAAGGAAATACAT	0.418																																																	0													110.0	113.0	112.0					1																	213415458		2203	4300	6503	SO:0001583	missense	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2639A>G	1.37:g.213415458A>G	ENSP00000355927:p.Lys880Arg	Somatic		WXS	Illumina GAIIx	Phase_I	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.889034	0.52014	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.44482	1.38;1.4;1.41;0.92	5.91	3.62	0.41486	Serine/threonine-protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100013	0.64402	D	0.000002	T	0.38427	0.1040	L	0.31578	0.945	0.46241	D	0.998942	P;P;P	0.50272	0.918;0.933;0.868	P;P;P	0.51516	0.555;0.672;0.596	T	0.06356	-1.0831	10	0.36615	T	0.2	-16.3804	8.9974	0.36061	0.7941:0.0:0.2059:0.0	.	668;880;868	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	R	668;880;868;583	ENSP00000442306:K668R;ENSP00000355927:K880R;ENSP00000355926:K868R;ENSP00000439282:K583R	ENSP00000355926:K868R	K	+	2	0	RPS6KC1	211482081	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.245000	0.58734	0.509000	0.28195	0.533000	0.62120	AAG		0.418	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3		NM_012424	
RUVBL1	8607	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	127816145	127816145	+	Silent	SNP	G	G	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr3:127816145G>T	ENST00000322623.5	-	8	1113	c.1014C>A	c.(1012-1014)atC>atA	p.I338I	RUVBL1_ENST00000464873.1_Silent_p.I278I|RUVBL1_ENST00000417360.1_Silent_p.I338I	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	338					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)			endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		CATCCTACCTGATGACACAGT	0.537																																																	0													53.0	54.0	53.0					3																	127816145		2203	4300	6503	SO:0001819	synonymous_variant	8607			AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"""INO80 complex subunits"", ""ATPases / AAA-type"""	10474	protein-coding gene	gene with protein product	"""pontin"", ""INO80 complex subunit H"""	603449	"""RuvB (E coli homolog)-like 1"", ""RuvB-like 1 (E. coli)"", ""RuvB-like AAA ATPase"""			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.1014C>A	3.37:g.127816145G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Silent	SNP	ENST00000322623.5	37	CCDS3047.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.555061	0.45487	.	.	ENSG00000175792	ENST00000472125	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	T	0.64427	0.2597	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62539	-0.6833	4	.	.	.	-9.824	12.3546	0.55167	0.0771:0.0:0.9229:0.0	.	.	.	.	K	158	.	.	Q	-	1	0	RUVBL1	129298835	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.067000	0.64357	2.476000	0.83614	0.591000	0.81541	CAG		0.537	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			
SETX	23064	hgsc.bcm.edu;ucsc.edu	37	9	135210042	135210042	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:135210042delT	ENST00000224140.5	-	7	973	c.791delA	c.(790-792)aatfs	p.N264fs	SETX_ENST00000372169.2_Frame_Shift_Del_p.N264fs|SETX_ENST00000393220.1_Frame_Shift_Del_p.N264fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	264					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CATAAAATCATTTTGTTTGTC	0.373																																																	0													177.0	146.0	156.0					9																	135210042		2203	4300	6503	SO:0001589	frameshift_variant	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.791delA	9.37:g.135210042delT	ENSP00000224140:p.Asn264fs	Somatic		WXS	Illumina HiSeq	Phase_I	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Del	DEL	ENST00000224140.5	37	CCDS6947.1																																																																																				0.373	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3		NM_015046	
SLC6A10P	386757	broad.mit.edu	37	16	32890622	32890622	+	RNA	SNP	T	T	G	rs200656321		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:32890622T>G	ENST00000330048.5	-	0	3176					NR_003083.2				solute carrier family 6 (neurotransmitter transporter), member 10, pseudogene																		CGTTGGTGTTTTTGTAGACCA	0.617																																																	0																																												386757			U41163		16p11.2	2013-07-19	2013-07-19	2013-07-19	ENSG00000214617	ENSG00000214617		"""Solute carriers"""	11043	pseudogene	pseudogene	"""creatine transporter-2"""		"""solute carrier family 6 (neurotransmitter transporter, creatine), member 10"""	SLC6A10		9154116	Standard	NR_003083		Approved	CT-2	uc002edh.1		OTTHUMG00000132481		16.37:g.32890622T>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000330048.5	37																																																																																					0.617	SLC6A10P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432081.2			
SLC6A17	388662	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	110709686	110709686	+	Silent	SNP	C	C	T	rs201199061		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:110709686C>T	ENST00000331565.4	+	2	620	c.135C>T	c.(133-135)ggC>ggT	p.G45G	RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	45					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GTGAGGCAGGCGGCAAGCAGA	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		14440	0.001		0.0	False		,,,				2504	0.0																0													63.0	51.0	55.0					1																	110709686		2203	4300	6503	SO:0001819	synonymous_variant	388662				CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.135C>T	1.37:g.110709686C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																				0.607	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2		XM_371280	
TBC1D4	9882	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	75936707	75936707	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr13:75936707T>A	ENST00000377636.3	-	2	881	c.535A>T	c.(535-537)Aaa>Taa	p.K179*	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Nonsense_Mutation_p.K179*|TBC1D4_ENST00000431480.2_Nonsense_Mutation_p.K179*	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	179	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		ATGGCCGCTTTAGATAATTGC	0.408																																																	0													158.0	149.0	152.0					13																	75936707		1848	4099	5947	SO:0001587	stop_gained	9882			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.535A>T	13.37:g.75936707T>A	ENSP00000366863:p.Lys179*	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Nonsense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	40	8.183816	0.98693	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	.	.	.	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.9717	15.3699	0.74554	0.0:0.0:0.0:1.0	.	.	.	.	X	179	.	ENSP00000366852:K179X	K	-	1	0	TBC1D4	74834708	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	7.693000	0.84214	2.036000	0.60181	0.455000	0.32223	AAA		0.408	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1		NM_014832	
TCHH	7062	hgsc.bcm.edu	37	1	152082257	152082257	+	Missense_Mutation	SNP	C	C	G	rs369695249		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:152082257C>G	ENST00000368804.1	-	2	3435	c.3436G>C	c.(3436-3438)Gtg>Ctg	p.V1146L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1146	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			tcctgctgcacctcctcttcc	0.607																																																	0													84.0	82.0	83.0					1																	152082257		2005	4164	6169	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3436G>C	1.37:g.152082257C>G	ENSP00000357794:p.Val1146Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	G	9.805	1.181577	0.21787	.	.	ENSG00000159450	ENST00000368804	T	0.02140	4.43	2.64	1.68	0.24146	.	.	.	.	.	T	0.00328	0.0010	N	0.01168	-0.975	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	9	0.27785	T	0.31	-5.6672	9.6623	0.39962	0.0:0.4132:0.5868:0.0	.	1146	Q07283	TRHY_HUMAN	L	1146	ENSP00000357794:V1146L	ENSP00000357794:V1146L	V	-	1	0	TCHH	150348881	0.003000	0.15002	0.020000	0.16555	0.396000	0.30629	0.542000	0.23222	-0.079000	0.12707	-0.371000	0.07208	GTG		0.607	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TCHH	7062	hgsc.bcm.edu	37	1	152082376	152082376	+	Missense_Mutation	SNP	C	C	A	rs200755879	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:152082376C>A	ENST00000368804.1	-	2	3316	c.3317G>T	c.(3316-3318)cGg>cTg	p.R1106L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1106	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGCCTCTCCCGCTCCTGGCG	0.612													C|||	54	0.0107827	0.0053	0.0	5008	,	,		22224	0.0456		0.0	False		,,,				2504	0.001																0								C	LEU/ARG	26,3924		0,26,1949	92.0	94.0	94.0		3317	-6.1	0.0	1		94	1,8273		0,1,4136	no	missense	TCHH	NM_007113.2	102	0,27,6085	AA,AC,CC		0.0121,0.6582,0.2209	benign	1106/1944	152082376	27,12197	1975	4137	6112	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3317G>T	1.37:g.152082376C>A	ENSP00000357794:p.Arg1106Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	5.178	0.218352	0.09810	0.006582	1.21E-4	ENSG00000159450	ENST00000368804	T	0.12361	2.69	3.07	-6.14	0.02111	.	.	.	.	.	T	0.01387	0.0045	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44528	-0.9322	9	0.26408	T	0.33	.	4.343	0.11119	0.4645:0.2516:0.0:0.2839	.	1106	Q07283	TRHY_HUMAN	L	1106	ENSP00000357794:R1106L	ENSP00000357794:R1106L	R	-	2	0	TCHH	150349000	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.957000	0.01521	-1.861000	0.01153	-1.305000	0.01319	CGG		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TCHH	7062	hgsc.bcm.edu	37	1	152082484	152082484	+	Missense_Mutation	SNP	G	G	T	rs377407296		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:152082484G>T	ENST00000368804.1	-	2	3208	c.3209C>A	c.(3208-3210)aCg>aAg	p.T1070K		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1070	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.T1070K(4)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			gcgccttctcgtctcccgttc	0.597																																																	4	Substitution - Missense(4)	endometrium(3)|skin(1)											108.0	112.0	111.0					1																	152082484		2000	4150	6150	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3209C>A	1.37:g.152082484G>T	ENSP00000357794:p.Thr1070Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	5.324	0.245208	0.10077	.	.	ENSG00000159450	ENST00000368804	T	0.04317	3.65	1.72	-1.62	0.08372	.	.	.	.	.	T	0.00356	0.0011	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37502	-0.9703	9	0.06099	T	0.92	.	4.3307	0.11062	0.0:0.1458:0.429:0.4252	.	1070	Q07283	TRHY_HUMAN	K	1070	ENSP00000357794:T1070K	ENSP00000357794:T1070K	T	-	2	0	TCHH	150349108	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-3.679000	0.00395	-1.676000	0.01457	-0.539000	0.04255	ACG		0.597	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TICAM1	148022	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	4817211	4817211	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:4817211T>A	ENST00000248244.5	-	2	1408	c.1179A>T	c.(1177-1179)aaA>aaT	p.K393N		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	393	TIR.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AGTTATAGAATTTCTGTTCCG	0.592																																																	0													44.0	46.0	45.0					19																	4817211		2203	4300	6503	SO:0001583	missense	148022			AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1179A>T	19.37:g.4817211T>A	ENSP00000248244:p.Lys393Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B3Y691|O75532|Q86XP8|Q96GA0	Missense_Mutation	SNP	ENST00000248244.5	37	CCDS12136.1	.	.	.	.	.	.	.	.	.	.	T	17.01	3.279634	0.59758	.	.	ENSG00000127666	ENST00000248244	T	0.02787	4.16	4.42	-8.02	0.01118	.	0.340155	0.17557	N	0.169948	T	0.02533	0.0077	L	0.44542	1.39	0.20403	N	0.999906	P	0.44877	0.845	B	0.43478	0.421	T	0.10291	-1.0636	10	0.66056	D	0.02	-22.9006	7.1305	0.25497	0.0:0.3566:0.149:0.4944	.	393	Q8IUC6	TCAM1_HUMAN	N	393	ENSP00000248244:K393N	ENSP00000248244:K393N	K	-	3	2	TICAM1	4768211	0.000000	0.05858	0.173000	0.22940	0.659000	0.38960	-3.344000	0.00504	-0.849000	0.04158	0.260000	0.18958	AAA		0.592	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1		NM_014261	
TMCO3	55002	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	114149939	114149939	+	Missense_Mutation	SNP	G	G	A	rs139520979	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr13:114149939G>A	ENST00000434316.2	+	2	402	c.43G>A	c.(43-45)Gtc>Atc	p.V15I	TMCO3_ENST00000375391.1_Missense_Mutation_p.V15I|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	15						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GCTGTTTCCCGTCCTTCCCTG	0.642													G|||	2	0.000399361	0.0	0.0	5008	,	,		15671	0.0		0.002	False		,,,				2504	0.0																0													90.0	82.0	85.0					13																	114149939		2203	4300	6503	SO:0001583	missense	55002			BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.43G>A	13.37:g.114149939G>A	ENSP00000389399:p.Val15Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.52	1.661796	0.29515	.	.	ENSG00000150403	ENST00000434316;ENST00000375391	T	0.30182	1.54	5.59	-10.6	0.00265	.	0.815504	0.11281	N	0.580293	T	0.12008	0.0292	N	0.22421	0.69	0.09310	N	1	B;B	0.15930	0.009;0.015	B;B	0.11329	0.002;0.006	T	0.10989	-1.0606	10	0.21014	T	0.42	-14.8361	5.1289	0.14899	0.0832:0.4219:0.2614:0.2335	.	15;15	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	I	15	ENSP00000389399:V15I	ENSP00000364540:V15I	V	+	1	0	TMCO3	113197940	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.805000	0.04530	-1.783000	0.01274	-1.737000	0.00689	GTC		0.642	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3		NM_017905	
SCTR	6344	hgsc.bcm.edu	37	2	120194651	120194652	+	IGR	INS	-	-	GTGTGC	rs3217464|rs201433053|rs201077606	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr2:120194651_120194652insGTGTGC	ENST00000019103.5	-	0	1865				TMEM37_ENST00000409826.1_In_Frame_Ins_p.82_82T>SVP|TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_In_Frame_Ins_p.70_70T>SVP	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)	p.T70>SVP(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CACCAACCAGACGATCTGCTTC	0.668														4489	0.896366	0.9705	0.8386	5008	,	,		15646	0.8919		0.8748	False		,,,				2504	0.864																1	Complex - insertion inframe(1)	ovary(1)								4023,213		1924,175,19						3.4	0.6		dbSNP_126	56	6958,1218		3018,922,148	no	coding	TMEM37	NM_183240.2		4942,1097,167	A1A1,A1R,RR		14.8973,5.0283,11.5292				10981,1431				SO:0001628	intergenic_variant	140738				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194651_120194652insGTGTGC		Somatic		WXS	Illumina HiSeq	Phase_I	Q12961|Q13213|Q53T00	In_Frame_Ins	INS	ENST00000019103.5	37	CCDS2127.1																																																																																				0.668	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			
TPRX1	284355	hgsc.bcm.edu	37	19	48305658	48305658	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:48305658G>A	ENST00000322175.3	-	2	765	c.610C>T	c.(610-612)Cca>Tca	p.P204S	TPRX1_ENST00000543508.1_Missense_Mutation_p.P194S|TPRX1_ENST00000535759.1_Missense_Mutation_p.P301S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	204	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		atcgggcctgggatcgggact	0.662																																					Esophageal Squamous(123;175 2281 3051 32395)												0																																										SO:0001583	missense	284355				CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.610C>T	19.37:g.48305658G>A	ENSP00000323455:p.Pro204Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	4.478	0.088566	0.08583	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.65549	-0.16;-0.16;-0.16	0.361	-0.722	0.11184	.	.	.	.	.	T	0.44414	0.1292	N	0.08118	0	0.09310	N	1	D	0.55172	0.97	P	0.50791	0.65	T	0.34700	-0.9818	8	0.46703	T	0.11	.	.	.	.	.	204	Q8N7U7	TPRX1_HUMAN	S	204;301;194	ENSP00000323455:P204S;ENSP00000438832:P301S;ENSP00000438712:P194S	ENSP00000323455:P204S	P	-	1	0	TPRX1	52997470	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-2.095000	0.01350	-0.452000	0.07087	-0.459000	0.05422	CCA		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1		NM_198479	
TTC12	54970	broad.mit.edu;ucsc.edu	37	11	113205696	113205696	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr11:113205696A>C	ENST00000529221.1	+	8	618	c.513A>C	c.(511-513)gaA>gaC	p.E171D	TTC12_ENST00000483239.2_Missense_Mutation_p.E177D|TTC12_ENST00000393020.1_Missense_Mutation_p.E171D|TTC12_ENST00000314756.3_Missense_Mutation_p.E171D	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	171										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		AGTGTGATGAAAAATGCACAA	0.388																																																	0													93.0	86.0	88.0					11																	113205696		2201	4296	6497	SO:0001583	missense	54970			AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.513A>C	11.37:g.113205696A>C	ENSP00000433757:p.Glu171Asp	Somatic		WXS	Illumina GAIIx	Phase_I	Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	CCDS8360.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113481	0.77210	.	.	ENSG00000149292	ENST00000529221;ENST00000442859;ENST00000531164;ENST00000529850;ENST00000314756;ENST00000393020;ENST00000483239	T;T;T;T;T;T;T	0.74002	1.58;-0.8;-0.8;-0.8;1.58;1.58;1.58	5.33	-5.55	0.02536	Tetratricopeptide-like helical (1);Armadillo-type fold (1);Tetratricopeptide repeat-containing (1);	0.287665	0.37348	N	0.002132	T	0.64918	0.2642	N	0.17564	0.495	0.37863	D	0.929774	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.989	T	0.66976	-0.5787	10	0.48119	T	0.1	-16.4339	3.5002	0.07670	0.3885:0.1136:0.3874:0.1106	.	171;171	A8K8G6;Q9H892	.;TTC12_HUMAN	D	171;171;146;151;171;171;177	ENSP00000433757:E171D;ENSP00000400039:E171D;ENSP00000433916:E146D;ENSP00000431806:E151D;ENSP00000315160:E171D;ENSP00000376743:E171D;ENSP00000419652:E177D	ENSP00000315160:E171D	E	+	3	2	TTC12	112710906	0.778000	0.28640	0.909000	0.35828	0.988000	0.76386	-0.098000	0.11024	-0.992000	0.03472	-0.385000	0.06624	GAA		0.388	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2		NM_017868	
UBB	7314	hgsc.bcm.edu	37	17	16285560	16285560	+	Silent	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:16285560T>C	ENST00000395837.1	+	2	520	c.339T>C	c.(337-339)ccT>ccC	p.P113P	UBB_ENST00000395839.1_Silent_p.P113P|UBB_ENST00000535788.1_Intron|UBB_ENST00000578649.1_Intron|UBB_ENST00000302182.3_Silent_p.P113P|RP11-138I1.4_ENST00000583934.1_RNA	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	113	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AAGGCATCCCTCCCGACCAGC	0.557																																					Melanoma(163;1126 3406 34901)												0													115.0	112.0	113.0					17																	16285560		2203	4300	6503	SO:0001819	synonymous_variant	7314				CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.339T>C	17.37:g.16285560T>C		Somatic		WXS	Illumina HiSeq	Phase_I	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																				0.557	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1		NM_018955	
UNC119	9094	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	26875651	26875651	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:26875651G>A	ENST00000335765.4	-	2	403	c.293C>T	c.(292-294)tCa>tTa	p.S98L	UNC119_ENST00000470125.1_Missense_Mutation_p.S3L|UNC119_ENST00000484980.1_Missense_Mutation_p.S3L|UNC119_ENST00000301032.4_Missense_Mutation_p.S98L	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	98					cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					GACAGTGCCTGAGTCCATGTC	0.547											OREG0024277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0													94.0	94.0	94.0					17																	26875651		2203	4300	6503	SO:0001583	missense	9094			U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103			12565	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog A (Chlamydomonas)"""	604011	"""unc119 (C.elegans) homolog"""			8576185, 9538874	Standard	NM_005148		Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.293C>T	17.37:g.26875651G>A	ENSP00000337040:p.Ser98Leu	Somatic	790	WXS	Illumina HiSeq	Phase_I	A8K8G4|F1T095|O95126	Missense_Mutation	SNP	ENST00000335765.4	37	CCDS11233.1	.	.	.	.	.	.	.	.	.	.	G	35	5.465656	0.96257	.	.	ENSG00000109103	ENST00000335765;ENST00000301032;ENST00000444148	T;T;T	0.79940	-1.23;-1.25;-1.32	5.94	3.97	0.46021	Immunoglobulin E-set (1);	0.056607	0.64402	D	0.000001	D	0.89462	0.6722	M	0.87827	2.91	0.58432	D	0.999995	D;D	0.76494	0.999;0.997	D;P	0.65140	0.932;0.839	D	0.90529	0.4494	10	0.87932	D	0	-5.2697	13.0643	0.59024	0.1131:0.0:0.8869:0.0	.	98;98	F1T095;Q13432	.;U119A_HUMAN	L	98;98;91	ENSP00000337040:S98L;ENSP00000301032:S98L;ENSP00000414639:S91L	ENSP00000301032:S98L	S	-	2	0	UNC119	23899778	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.869000	0.99810	0.863000	0.35553	0.557000	0.71058	TCA		0.547	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255842.2			
Unknown	0	broad.mit.edu	37	1	148891643	148891643	+	IGR	SNP	A	A	G	rs200975583		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:148891643A>G								RP11-763B22.6 (37926 upstream) : RNA5SP59 (21629 downstream)																							CCAAAACTGAAATTGAAGATT	0.423																																																	0																																										SO:0001628	intergenic_variant	0																															1.37:g.148891643A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.423									
Unknown	0	broad.mit.edu	37	12	92116	92116	+	IGR	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:92116C>T								AC215219.1 (18794 upstream) : AC026369.1 (54935 downstream)																							CAGCGCCAGGCAGTGGTGCAG	0.597																																																	0																																										SO:0001628	intergenic_variant	0																															12.37:g.92116C>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.597									
Unknown	0	broad.mit.edu	37	15	84945393	84945393	+	IGR	SNP	C	C	T	rs437422	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr15:84945393C>T								GOLGA6L4 (31273 upstream) : RN7SL417P (3376 downstream)																							TCCAACTCCTCCTCTCTGCAT	0.532													.|||	152	0.0303514	0.0234	0.147	5008	,	,		19025	0.0079		0.004	False		,,,				2504	0.0072																0																																										SO:0001628	intergenic_variant	0																															15.37:g.84945393C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.532									
LRRC37A4P	55073	broad.mit.edu	37	17	43625348	43625348	+	RNA	SNP	C	C	T	rs201776882	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:43625348C>T	ENST00000586411.1	-	0	1652				RP11-798G7.6_ENST00000586348.1_lincRNA																							AGTCAGGCTTCGATGCAGACT	0.498																																																	0																																												0																															17.37:g.43625348C>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000586411.1	37																																																																																					0.498	RP11-798G7.7-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000452150.1			
MIR4477B	100616194	broad.mit.edu	37	9	68413654	68413654	+	RNA	SNP	G	G	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr9:68413654G>A	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		GAGTGCAGACGAGAGCCCCGG	0.642																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68413654G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581659.1	37																																																																																					0.642	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
UQCRFS1	7386	broad.mit.edu	37	19	29699033	29699033	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:29699033T>C	ENST00000304863.4	-	2	669	c.247A>G	c.(247-249)Atc>Gtc	p.I83V		NM_006003.2	NP_005994.2	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	83					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)	p.I83V(4)		endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)			GGCACCTTGATGTCTGTGTGG	0.423																																																	4	Substitution - Missense(4)	endometrium(2)|kidney(2)											53.0	59.0	57.0					19																	29699033		2203	4299	6502	SO:0001583	missense	7386			BC010035	CCDS12415.1	19q12	2011-07-04			ENSG00000169021	ENSG00000169021	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12587	protein-coding gene	gene with protein product	"""cytochrome b-c1 complex subunit 5"""	191327				8088805	Standard	NM_006003		Approved	RIS1, RIP1, UQCR5, RISP	uc002nsd.2	P47985		ENST00000304863.4:c.247A>G	19.37:g.29699033T>C	ENSP00000306397:p.Ile83Val	Somatic		WXS	Illumina GAIIx	Phase_I	A8K519|Q6NVX5|Q9UPH2	Missense_Mutation	SNP	ENST00000304863.4	37	CCDS12415.1	.	.	.	.	.	.	.	.	.	.	t	0.014	-1.596233	0.00857	.	.	ENSG00000169021	ENST00000304863	T	0.42131	0.98	5.42	-4.98	0.03019	Ubiquinol cytochrome reductase, transmembrane domain (3);	0.618499	0.17385	N	0.176150	T	0.22360	0.0539	N	0.16862	0.45	0.20764	N	0.999851	B	0.02656	0.0	B	0.14578	0.011	T	0.23976	-1.0173	10	0.08837	T	0.75	.	17.2071	0.86921	0.0:0.6778:0.0:0.3222	.	83	P47985	UCRI_HUMAN	V	83	ENSP00000306397:I83V	ENSP00000306397:I83V	I	-	1	0	UQCRFS1	34390873	0.987000	0.35691	0.084000	0.20598	0.009000	0.06853	0.184000	0.16939	-1.243000	0.02519	-3.117000	0.00062	ATC		0.423	UQCRFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458563.1		NM_006003	
VCX2	51480	hgsc.bcm.edu	37	X	8138165	8138165	+	Missense_Mutation	SNP	C	C	G	rs1058237		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:8138165C>G	ENST00000317103.4	-	3	634	c.328G>C	c.(328-330)Gtg>Ctg	p.V110L		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	110	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		V -> L (in dbSNP:rs1058237). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCC	0.637													G|||	3167	0.83894	0.6505	0.6484	3775	,	,		3693	0.7242		0.5795	False		,,,				2504	0.5562																0													38.0	47.0	44.0					X																	8138165		2171	4239	6410	SO:0001583	missense	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.328G>C	X.37:g.8138165C>G	ENSP00000321309:p.Val110Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	1080	0.650994575045208	166	0.45108695652173914	133	0.5732758620689655	217	0.638235294117647	228	0.41155234657039713	G	0.004	-2.260355	0.00262	.	.	ENSG00000177504	ENST00000317103	T	0.12465	2.68	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39781	-0.9597	7	0.06099	T	0.92	.	.	.	.	rs1058237;rs3198852;rs16998641	110	Q9H322	VCX2_HUMAN	L	110	ENSP00000321309:V110L	ENSP00000321309:V110L	V	-	1	0	VCX2	8098165	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.675000	0.05227	-1.450000	0.01936	-1.461000	0.01025	GTG		0.637	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1		NM_016378	
VCX2	51480	hgsc.bcm.edu	37	X	8138170	8138171	+	Missense_Mutation	DNP	CT	CT	GC	rs75657421|rs78723459		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:8138170_8138171CT>GC	ENST00000317103.4	-	3	628_629	c.322_323AG>GC	c.(322-324)AGc>GCc	p.S108A		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	108	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.			S -> A (in Ref. 1; AAG41765, 2; AAF28172 and 4; AAH98113/AAH96715/AAH98163). {ECO:0000305}.						endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TTCCACCTCGCTCTCCTGACTC	0.644																																																	0																																										SO:0001583	missense	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.322_323delinsGC	X.37:g.8138170_8138171delinsGC	ENSP00000321309:p.Ser108Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1																																																																																				0.644	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1		NM_016378	
VCX2	51480	hgsc.bcm.edu	37	X	8138182	8138182	+	Missense_Mutation	SNP	A	A	G	rs41305169		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:8138182A>G	ENST00000317103.4	-	3	617	c.311T>C	c.(310-312)cTg>cCg	p.L104P		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	104	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		L -> P (in dbSNP:rs41305169). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CTCCTGACTCAGGGGGTCGTG	0.667																																																	0													27.0	34.0	32.0					X																	8138182		2157	4235	6392	SO:0001583	missense	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.311T>C	X.37:g.8138182A>G	ENSP00000321309:p.Leu104Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	798	0.4810126582278481	89	0.21394230769230768	103	0.3759124087591241	195	0.5158730158730159	169	0.2725806451612903	A	3.519	-0.098106	0.07010	.	.	ENSG00000177504	ENST00000317103	T	0.34859	1.34	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.09310	N	0.999999	D	0.54397	0.966	P	0.61070	0.883	T	0.47649	-0.9101	8	0.51188	T	0.08	.	.	.	.	rs41305169	104	Q9H322	VCX2_HUMAN	P	104	ENSP00000321309:L104P	ENSP00000321309:L104P	L	-	2	0	VCX2	8098182	0.001000	0.12720	0.014000	0.15608	0.015000	0.08874	-0.143000	0.10296	0.105000	0.17753	0.104000	0.15600	CTG		0.667	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1		NM_016378	
USP51	158880	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	55513642	55513642	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:55513642C>A	ENST00000500968.3	-	2	1813	c.1731G>T	c.(1729-1731)caG>caT	p.Q577H	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	577	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						TAGTAGACTCCTGGTAGCTTT	0.433																																																	0													64.0	55.0	58.0					X																	55513642		2203	4300	6503	SO:0001583	missense	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1731G>T	X.37:g.55513642C>A	ENSP00000423333:p.Gln577His	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	12.45	1.940680	0.34283	.	.	ENSG00000247746	ENST00000500968	T	0.03094	4.05	2.96	1.15	0.20763	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.19604	0.0471	M	0.93283	3.4	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.00364	-1.1787	10	0.59425	D	0.04	.	6.58	0.22588	0.0:0.7289:0.0:0.2711	.	577	Q70EK9	UBP51_HUMAN	H	577	ENSP00000423333:Q577H	ENSP00000423333:Q577H	Q	-	3	2	USP51	55530367	1.000000	0.71417	0.999000	0.59377	0.757000	0.42996	3.899000	0.56288	0.180000	0.19960	-0.458000	0.05436	CAG		0.433	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2		NM_201286	
DDX11L1	100287102	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	G	A	rs71252251	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:14976G>A	ENST00000456328.2	+	0	1657					NR_046018.2|NR_051986.1				DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1																		CTACCCTTGCGCCTCATGACC	0.582																																																	0																																												653635			AM992871		1p36.33	2012-02-23	2012-02-23		ENSG00000223972	ENSG00000223972			37102	pseudogene	pseudogene			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1"""			19476624	Standard	NR_046018		Approved		uc010nxq.1		OTTHUMG00000000961		1.37:g.14976G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000456328.2	37																																																																																					0.582	DDX11L1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000362751.1			
WNK3	65267	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	54319687	54319687	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chrX:54319687A>T	ENST00000375159.2	-	8	1766	c.1767T>A	c.(1765-1767)taT>taA	p.Y589*	WNK3_ENST00000375169.3_Nonsense_Mutation_p.Y589*|WNK3_ENST00000354646.2_Nonsense_Mutation_p.Y589*			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	589					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GATTTGAGGAATAGGCTACAC	0.403																																																	0													94.0	84.0	87.0					X																	54319687		2203	4300	6503	SO:0001587	stop_gained	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1767T>A	X.37:g.54319687A>T	ENSP00000364301:p.Tyr589*	Somatic		WXS	Illumina HiSeq	Phase_I	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Nonsense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	38	6.649758	0.97734	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	.	.	.	5.6	2.73	0.32206	.	0.128369	0.35677	N	0.003059	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.4894	7.8048	0.29195	0.7158:0.0:0.2842:0.0	.	.	.	.	X	589	.	ENSP00000346667:Y589X	Y	-	3	2	WNK3	54336412	1.000000	0.71417	0.950000	0.38849	0.924000	0.55760	1.741000	0.38238	0.703000	0.31848	0.481000	0.45027	TAT		0.403	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2		NM_020922	
XPOT	11260	broad.mit.edu	37	12	64812710	64812710	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:64812710T>C	ENST00000332707.5	+	6	854	c.325T>C	c.(325-327)Ttc>Ctc	p.F109L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	109	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		CGCCCAAGTCTTCGCCTTGCT	0.388																																																	0													95.0	92.0	93.0					12																	64812710		2203	4300	6503	SO:0001583	missense	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.325T>C	12.37:g.64812710T>C	ENSP00000327821:p.Phe109Leu	Somatic		WXS	Illumina GAIIx	Phase_I	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.787343	0.49997	.	.	ENSG00000184575	ENST00000332707;ENST00000400935	T;T	0.59364	0.27;0.27	4.78	4.78	0.61160	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.051754	0.85682	D	0.000000	T	0.44286	0.1286	L	0.27975	0.815	0.80722	D	1	B	0.14805	0.011	B	0.18561	0.022	T	0.30794	-0.9966	9	.	.	.	.	14.633	0.68671	0.0:0.0:0.0:1.0	.	109	O43592	XPOT_HUMAN	L	109	ENSP00000327821:F109L;ENSP00000383722:F109L	.	F	+	1	0	XPOT	63098977	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.199000	0.72112	1.918000	0.55548	0.455000	0.32223	TTC		0.388	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1		NM_007235	
XPOT	11260	broad.mit.edu;ucsc.edu	37	12	64812728	64812728	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:64812728A>G	ENST00000332707.5	+	6	872	c.343A>G	c.(343-345)Aca>Gca	p.T115A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	115	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)	p.T115A(2)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GCTTTTTGTTACAGAGTATCT	0.433																																																	2	Substitution - Missense(2)	kidney(2)											108.0	103.0	105.0					12																	64812728		2203	4300	6503	SO:0001583	missense	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.343A>G	12.37:g.64812728A>G	ENSP00000327821:p.Thr115Ala	Somatic		WXS	Illumina GAIIx	Phase_I	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	A	7.950	0.744725	0.15710	.	.	ENSG00000184575	ENST00000332707;ENST00000400935	T;T	0.39406	1.08;1.08	4.78	4.78	0.61160	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.149484	0.64402	D	0.000017	T	0.19046	0.0457	N	0.02296	-0.605	0.46356	D	0.999	B	0.18610	0.029	B	0.14578	0.011	T	0.09596	-1.0667	9	.	.	.	.	14.633	0.68671	1.0:0.0:0.0:0.0	.	115	O43592	XPOT_HUMAN	A	115	ENSP00000327821:T115A;ENSP00000383722:T115A	.	T	+	1	0	XPOT	63098995	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.253000	0.78320	1.918000	0.55548	0.455000	0.32223	ACA		0.433	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1		NM_007235	
XPOT	11260	broad.mit.edu	37	12	64812808	64812808	+	Silent	SNP	C	C	G			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr12:64812808C>G	ENST00000332707.5	+	6	952	c.423C>G	c.(421-423)ctC>ctG	p.L141L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	141	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)	p.L141L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GAGTAGATCTCTACCTGCGAA	0.398																																																	1	Substitution - coding silent(1)	kidney(1)											129.0	128.0	128.0					12																	64812808		2203	4300	6503	SO:0001819	synonymous_variant	11260			AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.423C>G	12.37:g.64812808C>G		Somatic		WXS	Illumina GAIIx	Phase_I	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																				0.398	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1		NM_007235	
ZMYM4	9202	broad.mit.edu;ucsc.edu	37	1	35853066	35853066	+	Silent	SNP	T	T	C			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:35853066T>C	ENST00000314607.6	+	13	2204	c.2124T>C	c.(2122-2124)ttT>ttC	p.F708F	ZMYM4_ENST00000373297.2_Silent_p.F619F	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	708					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCAAAATGTTTCAGTTCTGTG	0.294																																																	0													52.0	57.0	55.0					1																	35853066		2203	4300	6503	SO:0001819	synonymous_variant	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2124T>C	1.37:g.35853066T>C		Somatic		WXS	Illumina GAIIx	Phase_I	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Silent	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	T	7.343	0.621231	0.14193	.	.	ENSG00000146463	ENST00000457946	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	T	0.60314	0.2259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59685	-0.7408	4	.	.	.	-15.417	8.9969	0.36059	0.0:0.0914:0.0:0.9086	.	.	.	.	P	368	.	.	S	+	1	0	ZMYM4	35625653	0.999000	0.42202	1.000000	0.80357	0.954000	0.61252	0.858000	0.27845	2.021000	0.59480	0.533000	0.62120	TCA		0.294	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3		NM_005095	
ZNF286B	729288	broad.mit.edu;ucsc.edu	37	17	18584142	18584142	+	Splice_Site	SNP	A	A	G	rs116808485	byFrequency	TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr17:18584142A>G	ENST00000545289.1	-	3	288	c.38T>C	c.(37-39)gTt>gCt	p.V13A	ZNF286B_ENST00000285274.5_Splice_Site_p.V13A	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						GGAAGACAGAACTAACGACAA	0.473																																																	0													116.0	118.0	118.0					17																	18584142		692	1591	2283	SO:0001630	splice_region_variant	729288				CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.38-1T>C	17.37:g.18584142A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																				0.473	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			XM_001723047	Missense_Mutation
ZSCAN32	54925	broad.mit.edu;ucsc.edu	37	16	3432991	3432991	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr16:3432991C>T	ENST00000396852.4	-	7	2262	c.1955G>A	c.(1954-1956)cGa>cAa	p.R652Q	ZSCAN32_ENST00000396846.3_Missense_Mutation_p.R652Q|ZSCAN32_ENST00000439568.2_Missense_Mutation_p.R363Q|ZSCAN32_ENST00000304926.3_Missense_Mutation_p.R440Q|NAA60_ENST00000576906.1_Intron	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	652					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)										GTGGGTTTTTCGGTGGGCACT	0.512																																																	0													110.0	96.0	101.0					16																	3432991		2197	4300	6497	SO:0001583	missense	0			AK000424	CCDS10503.1, CCDS66920.1, CCDS66921.1	16p13.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000140987	ENSG00000140987		"""-"", ""Zinc fingers, C2H2-type"""	20812	protein-coding gene	gene with protein product			"""zinc finger protein 434"""	ZNF434			Standard	XM_005255402		Approved	FLJ20417	uc002cux.4	Q9NX65	OTTHUMG00000129357	ENST00000396852.4:c.1955G>A	16.37:g.3432991C>T	ENSP00000380061:p.Arg652Gln	Somatic		WXS	Illumina GAIIx	Phase_I	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	37		.	.	.	.	.	.	.	.	.	.	C	0.496	-0.873324	0.02570	.	.	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000439568	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	3.18	0.858	0.19030	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04770	0.0129	N	0.04132	-0.27	0.21105	N	0.999784	B;P	0.37573	0.241;0.6	B;B	0.32342	0.021;0.144	T	0.25222	-1.0138	9	0.02654	T	1	.	5.3883	0.16229	0.0:0.2969:0.0:0.7031	.	440;652	Q9NX65;Q6WMU8	ZN434_HUMAN;.	Q	440;652;652;363	ENSP00000302502:R440Q;ENSP00000380061:R652Q;ENSP00000380057:R652Q;ENSP00000391787:R363Q	ENSP00000302502:R440Q	R	-	2	0	ZNF434	3372992	0.000000	0.05858	0.298000	0.25002	0.931000	0.56810	-0.020000	0.12525	0.176000	0.19873	-0.471000	0.05019	CGA		0.512	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2		NM_017810	
ZNF493	284443	broad.mit.edu	37	19	21607481	21607482	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:21607481_21607482delAA	ENST00000355504.4	+	2	1902_1903	c.1636_1637delAA	c.(1636-1638)aaafs	p.K546fs	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Frame_Shift_Del_p.K674fs	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	546					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						AACCCTTACTAAACATAAGATA	0.361																																																	0																																										SO:0001589	frameshift_variant	284443			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1636_1637delAA	19.37:g.21607481_21607482delAA	ENSP00000347691:p.Lys546fs	Somatic		WXS	Illumina GAIIx	Phase_I	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Frame_Shift_Del	DEL	ENST00000355504.4	37	CCDS12412.1																																																																																				0.361	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1		NM_175910	
ZNF610	162963	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	52857566	52857566	+	Silent	SNP	C	C	T			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr19:52857566C>T	ENST00000403906.3	+	5	709	c.253C>T	c.(253-255)Ctg>Ttg	p.L85L	ZNF610_ENST00000601151.1_Intron|ZNF610_ENST00000321287.8_Silent_p.L85L|ZNF610_ENST00000327920.8_Silent_p.L85L	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		GCCCTTGATTCTGCAAAGTCA	0.413																																																	0													85.0	88.0	87.0					19																	52857566		2203	4300	6503	SO:0001819	synonymous_variant	162963			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.253C>T	19.37:g.52857566C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																				0.413	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1		NM_173530	
ZFP69B	65243	broad.mit.edu	37	1	40922615	40922616	+	Splice_Site	DEL	AG	AG	-			TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr1:40922615_40922616delAG	ENST00000411995.2	+	4	588		c.e4-1		ZFP69B_ENST00000484445.1_Splice_Site|ZFP69B_ENST00000361584.3_Splice_Site	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTGATGTTCTAGGAACTGTTAA	0.485																																																	0																																										SO:0001630	splice_region_variant	0			BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	28053	protein-coding gene	gene with protein product			"""zinc finger protein 643"""	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.214-1AG>-	1.37:g.40922615_40922616delAG		Somatic		WXS	Illumina GAIIx	Phase_I	Q5QPL4	Splice_Site	DEL	ENST00000411995.2	37	CCDS452.2																																																																																				0.485	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2		NM_023070	Intron
ZSWIM3	140831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	44506358	44506358	+	Silent	SNP	G	G	A	rs149497744		TCGA-CJ-4643-01A-02D-1386-10	TCGA-CJ-4643-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e00e420-94fd-4115-9cd9-cef24f6df0eb	0e427f57-9cae-40dc-9a75-6387da9af195	g.chr20:44506358G>A	ENST00000255152.2	+	2	1370	c.1161G>A	c.(1159-1161)gcG>gcA	p.A387A	ZSWIM3_ENST00000454862.2_Silent_p.A381A	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	387							zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				GCCTGCTTGCGTGTAACACCT	0.547																																																	0								G		1,4405	2.1+/-5.4	0,1,2202	99.0	78.0	85.0		1161	-10.8	0.0	20	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	ZSWIM3	NM_080752.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		387/697	44506358	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140831			AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"""Zinc fingers, SWIM-type"""	16157	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 174"""		"""chromosome 20 open reading frame 164"""	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1161G>A	20.37:g.44506358G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q9BR13	Silent	SNP	ENST00000255152.2	37	CCDS13381.1																																																																																				0.547	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1		NM_080752	
