#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IGV	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_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_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
PTCHD2	57540	mdanderson.org	37	1	11586864	11586864	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:11586864G>A	ENST00000294484.6	+	13	2908	c.2770G>A	c.(2770-2772)Gtg>Atg	p.V924M	PTCHD2_ENST00000389575.3_Missense_Mutation_p.V924M	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	924					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CAGCTTCTACGTGGCCACCAA	0.607																																					p.V924M													.	.			0			c.G2770A												33.0	38.0	37.0					1																	11586864		2077	4205	6282	SO:0001583	missense	57540	exon13			TTCTACGTGGCCA	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.2770G>A	1.37:g.11586864G>A	ENSP00000294484:p.Val924Met		33	0	0		31	0.10	3	NM_020780	9	0.00	0	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611001	0.87258	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.92348	-3.02;-3.02	5.58	5.58	0.84498	.	0.157033	0.42682	D	0.000672	D	0.90143	0.6920	L	0.29908	0.895	0.38869	D	0.956653	D	0.55385	0.971	P	0.47206	0.541	D	0.91941	0.5563	10	0.66056	D	0.02	-17.7905	18.5585	0.91093	0.0:0.0:1.0:0.0	.	924	Q9P2K9	PTHD2_HUMAN	M	924	ENSP00000294484:V924M;ENSP00000374226:V924M	ENSP00000294484:V924M	V	+	1	0	PTCHD2	11509451	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.589000	0.74080	2.622000	0.88805	0.462000	0.41574	GTG			0.607	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000005770.2		XM_052561	
ESPNP	284729	broad.mit.edu	37	1	17030903	17030905	+	RNA	DEL	GAG	GAG	-	rs67156338|rs376609585	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	GAG	GAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:17030903_17030905delGAG	ENST00000492551.1	-	0	696					NR_026567.1				espin pseudogene																		AGAGATCGACGAGGAGGGGGCCT	0.64														1867	0.372804	0.3245	0.3343	5008	,	,		43669	0.4474		0.3936	False		,,,				2504	0.3671				.													.	.			0			.																																											0	.			ATCGACGAGGAGG	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17030906_17030908delGAG			11	0	0		7	0.71	5	.	0		0		RNA	DEL	ENST00000492551.1	37																																																																																						0.640	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000326311.1			
PI4KB	5298	mdanderson.org	37	1	151288391	151288391	+	Missense_Mutation	SNP	A	A	T	rs1752379	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:151288391A>T	ENST00000368873.1	-	2	735	c.567T>A	c.(565-567)gaT>gaA	p.D189E	PI4KB_ENST00000529142.1_Intron|PI4KB_ENST00000368875.2_Missense_Mutation_p.D201E|PI4KB_ENST00000368874.4_Missense_Mutation_p.D189E|PI4KB_ENST00000271657.5_Missense_Mutation_p.D201E|PI4KB_ENST00000368872.1_Missense_Mutation_p.D189E			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	189	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CATCACCCACATCCTCATCCA	0.512																																					p.D201E	Colon(154;765 1838 9854 28443 37492)												.	.			0			c.T603A												118.0	105.0	109.0					1																	151288391		2203	4300	6503	SO:0001583	missense	5298	exon3			ACCCACATCCTCA	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368873.1:c.567T>A	1.37:g.151288391A>T	ENSP00000357867:p.Asp189Glu		73	0	0		99	0.03	3	NM_002651	51	0.00	0	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Missense_Mutation	SNP	ENST00000368873.1	37		.	.	.	.	.	.	.	.	.	.	G	12.46	1.943169	0.34283	.	.	ENSG00000143393	ENST00000368874;ENST00000368875;ENST00000271657;ENST00000368873;ENST00000368872;ENST00000438243	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	4.98	-2.7	0.06004	.	0.052266	0.85682	D	0.000000	T	0.12263	0.0298	L	0.37630	1.12	0.21256	P	0.999745329	P;B;B	0.37500	0.597;0.008;0.025	B;B;B	0.35813	0.211;0.005;0.05	T	0.13045	-1.0524	9	0.22109	T	0.4	-20.1779	11.8956	0.52654	0.5982:0.0:0.4018:0.0	.	189;189;189	E9PIH4;Q9UBF8;Q9UBF8-2	.;PI4KB_HUMAN;.	E	189;201;201;189;189;189	ENSP00000357868:D189E;ENSP00000357869:D201E;ENSP00000271657:D201E;ENSP00000357867:D189E;ENSP00000357866:D189E;ENSP00000394719:D189E	ENSP00000271657:D201E	D	-	3	2	PI4KB	149555015	0.080000	0.21391	0.959000	0.39883	0.981000	0.71138	-0.730000	0.04915	-0.744000	0.04778	-1.082000	0.02213	GAT			0.512	PI4KB-002	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000034400.3		NM_002651	
SUMO1P2	474337	bcgsc.ca	37	1	168867522	168867522	+	IGR	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:168867522C>T								LINC00626 (105398 upstream) : LINC00970 (5620 downstream)																							CTCAAAGAATCATACTGTCAA	0.373																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	474337	.			AAGAATCATACTG																													1.37:g.168867522C>T			39	0	0		75	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.373										
BRINP2	57795	broad.mit.edu	37	1	177247722	177247722	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:177247722A>G	ENST00000361539.4	+	7	1348	c.1036A>G	c.(1036-1038)Agg>Ggg	p.R346G	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	346					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											CCTGCTGAAAAGGCTGCCCGA	0.592																																					p.R346G													.	FAM5B	191		0			c.A1036G												156.0	166.0	163.0					1																	177247722		2203	4300	6503	SO:0001583	missense	0	exon7			CTGAAAAGGCTGC		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1036A>G	1.37:g.177247722A>G	ENSP00000354481:p.Arg346Gly		172	0.0058139535	1		265	0.02	5	NM_021165	0		0	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.782534	0.49891	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.18960	2.18	5.27	-2.5	0.06384	.	0.053205	0.64402	D	0.000001	T	0.36580	0.0972	M	0.67397	2.05	0.40841	D	0.983675	D;P;P	0.63046	0.992;0.915;0.598	P;P;B	0.59357	0.856;0.653;0.247	T	0.52223	-0.8604	10	0.87932	D	0	-9.5553	15.9782	0.80086	0.3875:0.6125:0.0:0.0	.	96;241;346	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	G	96;346	ENSP00000354481:R346G	ENSP00000354481:R346G	R	+	1	2	FAM5B	175514345	0.995000	0.38212	0.941000	0.38009	0.918000	0.54935	1.763000	0.38461	-0.019000	0.14055	0.533000	0.62120	AGG			0.592	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000084599.1		NM_021165	
PHLDA3	23612	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	201437676	201437676	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:201437676delC	ENST00000367311.3	-	1	636	c.239delG	c.(238-240)ggcfs	p.G81fs	PHLDA3_ENST00000367309.1_Frame_Shift_Del_p.G81fs|PHLDA3_ENST00000485436.1_5'UTR	NM_012396.3	NP_036528.1	Q9Y5J5	PHLA3_HUMAN	pleckstrin homology-like domain, family A, member 3	81	PH.				anatomical structure morphogenesis (GO:0009653)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-5-phosphate binding (GO:0010314)			lung(1)|prostate(1)	2						GATCTCGCCGCCCCCTTCGGT	0.657																																					p.G80fs													PHLDA3,colon,carcinoma,0,1	PHLDA3	11		0			c.240delC												66.0	71.0	69.0					1																	201437676		2203	4300	6503	SO:0001589	frameshift_variant	23612	exon1			TCGCCGCCCCCTT	AF151100	CCDS1412.1	1q31	2008-07-18			ENSG00000174307	ENSG00000174307			8934	protein-coding gene	gene with protein product	"""pleckstrin homology-like domain, family A, member 2"""	607054					Standard	NM_012396		Approved	TIH1	uc031prm.1	Q9Y5J5	OTTHUMG00000035767	ENST00000367311.3:c.239delG	1.37:g.201437676delC	ENSP00000356280:p.Gly81fs		289	0	0		241	0.29	71	NM_012396	290	0.00	0	B2R5A4|Q53HD6|Q8NBW9	Frame_Shift_Del	DEL	ENST00000367311.3	37	CCDS1412.1																																																																																					0.657	PHLDA3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000087020.2		NM_012396	
ERO1LB	56605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	236389708	236389708	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr1:236389708A>C	ENST00000354619.5	-	12	1114	c.913T>G	c.(913-915)Ttt>Gtt	p.F305V		NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	305					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	AAGTATAAAAAGTAAAGATTC	0.428																																					p.F305V													.	.			0			c.T913G												94.0	98.0	97.0					1																	236389708		2203	4300	6503	SO:0001583	missense	56605	exon12			ATAAAAAGTAAAG	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.913T>G	1.37:g.236389708A>C	ENSP00000346635:p.Phe305Val		164	0	0		226	0.31	70	NM_019891	5	0.20	1	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.699042	0.88830	.	.	ENSG00000086619	ENST00000354619;ENST00000264181	T;T	0.56941	0.43;0.43	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.77778	0.4181	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82739	-0.0308	10	0.66056	D	0.02	-24.8285	15.7024	0.77552	1.0:0.0:0.0:0.0	.	305	Q86YB8	ERO1B_HUMAN	V	305;30	ENSP00000346635:F305V;ENSP00000264181:F30V	ENSP00000264181:F30V	F	-	1	0	ERO1LB	234456331	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.933000	0.92911	2.109000	0.64355	0.472000	0.43445	TTT			0.428	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000096371.1		NM_019891	
EBF3	253738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	10	131676058	131676058	+	Missense_Mutation	SNP	T	T	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr10:131676058T>G	ENST00000355311.5	-	7	682	c.610A>C	c.(610-612)Aac>Cac	p.N204H	EBF3_ENST00000368648.3_Missense_Mutation_p.N204H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	204	Interaction with DNA. {ECO:0000250}.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TCTCGAGGGTTGCCTGCATTC	0.363																																					p.N204H													.	.			0			c.A610C												119.0	106.0	111.0					10																	131676058		2203	4300	6503	SO:0001583	missense	253738	exon7			GAGGGTTGCCTGC		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.610A>C	10.37:g.131676058T>G	ENSP00000347463:p.Asn204His		46	0	0		72	0.08	6	NM_001005463	27	0.04	1	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	T	23.7	4.444366	0.83993	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.61392	0.11;0.22	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.69415	0.3108	M	0.83953	2.67	0.80722	D	1	P	0.34837	0.472	B	0.43950	0.437	T	0.74481	-0.3651	10	0.87932	D	0	-21.4423	14.8999	0.70670	0.0:0.0:0.0:1.0	.	204	Q9H4W6-2	.	H	204	ENSP00000347463:N204H;ENSP00000357637:N204H	ENSP00000347463:N204H	N	-	1	0	EBF3	131566048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	1.915000	0.55452	0.460000	0.39030	AAC			0.363	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000051015.2		NM_001005463	
MUC2	4583	mdanderson.org	37	11	1092971	1092971	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:1092971C>T	ENST00000441003.2	+	30	4817	c.4790C>T	c.(4789-4791)aCa>aTa	p.T1597I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron	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)	ccaaccccaacacccaccggc	0.632																																					p.T1597I													MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2_ENST00000441003	0	1	0			c.C4790T												47.0	82.0	70.0					11																	1092971		1782	3233	5015	SO:0001583	missense	4583	exon30			CCCCAACACCCAC	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.4790C>T	11.37:g.1092971C>T	ENSP00000415183:p.Thr1597Ile		40	0	0		27	0.11	3	NM_002457	0		0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.395	-0.338980	0.05243	.	.	ENSG00000198788	ENST00000441003	T	0.14640	2.49	1.75	0.762	0.18454	.	.	.	.	.	T	0.07143	0.0181	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.41520	-0.9504	8	0.22109	T	0.4	.	4.3366	0.11089	0.0:0.6142:0.0:0.3858	.	1597	E7EUV1	.	I	1597	ENSP00000415183:T1597I	ENSP00000415183:T1597I	T	+	2	0	MUC2	1082971	0.029000	0.19370	0.001000	0.08648	0.134000	0.20937	1.107000	0.31110	0.104000	0.17725	0.121000	0.15741	ACA			0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000345894.2		NM_002457	
CDKN1C	1028	mdanderson.org	37	11	2906574	2906574	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:2906574C>T	ENST00000414822.3	-	1	537	c.146G>A	c.(145-147)cGc>cAc	p.R49H	CDKN1C_ENST00000440480.2_Missense_Mutation_p.R38H|CDKN1C_ENST00000430149.2_Missense_Mutation_p.R49H|CDKN1C_ENST00000380725.1_Missense_Mutation_p.R38H|CDKN1C_ENST00000313407.6_Missense_Mutation_p.R38H	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	49					adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCGGCCAGGCGGGCCTGCAG	0.697																																					p.R49H	GBM(111;59 1151 2497 5746 16112 18241 29216)												.	.			0			c.G146A												17.0	14.0	15.0					11																	2906574		2181	4285	6466	SO:0001583	missense	1028	exon1			GCCAGGCGGGCCT	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"""Beckwith-Wiedemann syndrome"""	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.146G>A	11.37:g.2906574C>T	ENSP00000413720:p.Arg49His		46	0	0		24	0.08	2	NM_000076	51	0.00	0		Missense_Mutation	SNP	ENST00000414822.3	37	CCDS7738.1	.	.	.	.	.	.	.	.	.	.	c	12.87	2.068563	0.36470	.	.	ENSG00000129757	ENST00000380725;ENST00000414822;ENST00000440480;ENST00000313407;ENST00000430149	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	2.49	0.326	0.15908	.	.	.	.	.	T	0.80037	0.4550	N	0.20685	0.6	0.19300	N	0.999974	D;D	0.89917	1.0;0.999	D;D	0.71656	0.945;0.974	T	0.66464	-0.5917	9	0.45353	T	0.12	.	3.9791	0.09487	0.0:0.5363:0.2321:0.2316	.	38;49	A6NK88;P49918	.;CDN1C_HUMAN	H	38;49;38;38;49	ENSP00000370101:R38H;ENSP00000413720:R49H;ENSP00000411257:R38H;ENSP00000321019:R38H;ENSP00000411552:R49H	ENSP00000321019:R38H	R	-	2	0	CDKN1C	2863150	0.999000	0.42202	0.999000	0.59377	0.966000	0.64601	1.193000	0.32162	0.333000	0.23563	0.298000	0.19748	CGC			0.697	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000027774.2		NM_000076	
TTC17	55761	ucsc.edu	37	11	43465665	43465665	+	Silent	SNP	G	G	A	rs377088555		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:43465665G>A	ENST00000039989.4	+	18	2585	c.2571G>A	c.(2569-2571)ggG>ggA	p.G857G	TTC17_ENST00000299240.6_Silent_p.G914G|TTC17_ENST00000526774.1_3'UTR	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	857					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						AAACTCCTGGGAAAAAAGTAG	0.433																																					p.G857G													.	TTC17	112		0			c.G2571A												79.0	78.0	78.0					11																	43465665		2203	4300	6503	SO:0001819	synonymous_variant	55761	exon18			TCCTGGGAAAAAA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2571G>A	11.37:g.43465665G>A			167	0	0		151	0.01	1	NM_018259	63	0.13	8	G3XAB3|Q8NEC0	Silent	SNP	ENST00000039989.4	37	CCDS31466.1																																																																																					0.433	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000389577.2		NM_018259	
FADS1	3992	mdanderson.org	37	11	61584183	61584183	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:61584183G>T	ENST00000350997.7	-	1	451	c.219C>A	c.(217-219)acC>acA	p.T73T	FADS2_ENST00000574708.1_Intron|FADS2_ENST00000522056.1_Intron|FADS1_ENST00000542506.1_5'Flank|FADS2_ENST00000257261.6_Intron|MIR1908_ENST00000410394.1_RNA|FADS2_ENST00000517839.1_Intron|FADS2_ENST00000522639.1_Intron|FADS1_ENST00000541683.1_5'Flank|FADS1_ENST00000433932.1_5'Flank	NM_013402.4	NP_037534.3	O60427	FADS1_HUMAN	fatty acid desaturase 1	16	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)	p.T16T(1)		central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AGTAGCGCGGGGTAGGTCCCT	0.711																																					p.T73T													FADS1,brain,glioma,0,1	FADS1	0	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C219A												7.0	8.0	8.0					11																	61584183		1876	4067	5943	SO:0001819	synonymous_variant	3992	exon1			GCGCGGGGTAGGT		CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"""Fatty acid desaturases"""	3574	protein-coding gene	gene with protein product	"""delta-5 desaturase"""	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000350997.7:c.219C>A	11.37:g.61584183G>T			88	0	0		42	0.07	3	NM_013402	11	0.00	0	A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	Silent	SNP	ENST00000350997.7	37	CCDS8011.2	.	.	.	.	.	.	.	.	.	.	G	8.885	0.952479	0.18431	.	.	ENSG00000149485	ENST00000491310	.	.	.	3.08	-3.13	0.05266	.	.	.	.	.	T	0.17959	0.0431	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	T	0.25222	-1.0138	4	.	.	.	-32.1774	1.0184	0.01513	0.1941:0.1287:0.2992:0.3781	.	.	.	.	H	23	.	.	P	-	2	0	FADS1	61340759	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-1.068000	0.03447	-0.641000	0.05487	-0.367000	0.07326	CCC			0.711	FADS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000347648.2		NM_013402	
Unknown	0	bcgsc.ca	37	11	62815368	62815368	+	IGR	SNP	G	G	A	rs150679703|rs374048942|rs7125680|rs372143980	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:62815368G>A								SLC22A8 (32057 upstream) : SLC22A24 (32043 downstream)																							CCAAGGTGCAGCATGCCATGT	0.562																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGTGCAGCATGCC																													11.37:g.62815368G>A			25	0	0		28	0.18	5	.	0		0		RNA	SNP		37																																																																																					0	0.562										
DPP3	10072	mdanderson.org	37	11	66276689	66276689	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:66276689G>T	ENST00000360510.2	+	18	2246	c.2181G>T	c.(2179-2181)aaG>aaT	p.K727N	BBS1_ENST00000393994.2_5'Flank|DPP3_ENST00000541961.1_Missense_Mutation_p.K727N|BBS1_ENST00000318312.7_5'Flank|DPP3_ENST00000531863.1_Missense_Mutation_p.K747N|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.R21M|DPP3_ENST00000453114.1_Missense_Mutation_p.K727N|DPP3_ENST00000530165.1_Missense_Mutation_p.K697N|DPP3_ENST00000532677.1_Missense_Mutation_p.K746N|BBS1_ENST00000455748.2_5'Flank|BBS1_ENST00000537537.1_5'Flank			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	727					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						GATTCTGGAAGGGCCCCAGTG	0.597																																					p.K727N													.	.			0			c.G2181T												29.0	27.0	28.0					11																	66276689		2200	4295	6495	SO:0001583	missense	10072	exon18			CTGGAAGGGCCCC	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.2181G>T	11.37:g.66276689G>T	ENSP00000353701:p.Lys727Asn		61	0	0		56	0.05	3	NM_005700	108	0.00	0	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.79|11.79	1.743883|1.743883	0.30865|0.30865	.|.	.|.	ENSG00000254986|ENSG00000256349	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000530165;ENST00000543807;ENST00000347422|ENST00000419755	T;T;T;T;T;T|D	0.19250|0.97138	2.16;2.17;2.18;2.18;2.18;2.18|-4.26	5.09|5.09	3.12|3.12	0.35913|0.35913	.|.	0.452030|.	0.24757|.	N|.	0.035859|.	D|D	0.91994|0.91994	0.7464|0.7464	N|N	0.08118|0.08118	0|0	0.21445|0.21445	N|N	0.999682|0.999682	B;B|P	0.26258|0.37276	0.145;0.026|0.589	B;B|B	0.26969|0.41036	0.075;0.021|0.346	D|D	0.86253|0.86253	0.1650|0.1650	10|9	0.87932|0.62326	D|D	0|0.03	.|.	7.4167|7.4167	0.27048|0.27048	0.2147:0.0:0.7853:0.0|0.2147:0.0:0.7853:0.0	.|.	746;727|21	G3V1D3;Q9NY33|Q8NFJ9-2	.;DPP3_HUMAN|.	N|M	747;746;727;727;727;697;625;307|21	ENSP00000432782:K747N;ENSP00000435284:K746N;ENSP00000353701:K727N;ENSP00000389943:K727N;ENSP00000440502:K727N;ENSP00000436941:K697N|ENSP00000398526:R21M	ENSP00000309957:K307N|ENSP00000398526:R21M	K|R	+|+	3|2	2|0	DPP3|CTD-3074O7.11	66033265|66033265	0.666000|0.666000	0.27475|0.27475	0.957000|0.957000	0.39632|0.39632	0.554000|0.554000	0.35429|0.35429	1.234000|1.234000	0.32660|0.32660	0.492000|0.492000	0.27815|0.27815	-0.377000|-0.377000	0.06932|0.06932	AAG|AGG			0.597	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000393424.2			
TMPRSS13	84000	mdanderson.org	37	11	117780545	117780545	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:117780545A>G	ENST00000430170.2	-	8	1172	c.1085T>C	c.(1084-1086)cTc>cCc	p.L362P	TMPRSS13_ENST00000524993.1_Missense_Mutation_p.L362P|TMPRSS13_ENST00000445164.2_Missense_Mutation_p.L362P|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.L362P|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.L327P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	362	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGCGGCAGTGAGCACCCACTG	0.622																																					p.L362P													.	.			0			c.T1085C												46.0	53.0	50.0					11																	117780545		2107	4250	6357	SO:0001583	missense	84000	exon8			GCAGTGAGCACCC	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.1085T>C	11.37:g.117780545A>G	ENSP00000387702:p.Leu362Pro		57	0	0		25	0.12	3	NM_001206790	5	0.00	0	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.981541	0.53827	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	T;T;T;T;D	0.92199	-1.2;-1.2;-1.2;-1.2;-2.99	4.51	4.51	0.55191	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.253869	0.27941	N	0.017226	D	0.96870	0.8978	H	0.96943	3.91	0.80722	D	1	P;P;D;P	0.76494	0.678;0.782;0.999;0.628	B;B;D;B	0.72338	0.345;0.187;0.977;0.317	D	0.96823	0.9605	10	0.87932	D	0	.	8.4031	0.32599	0.9103:0.0:0.0897:0.0	.	357;357;357;362	E9PHM4;Q9BYE2-4;Q9BYE2;E9PRA0	.;.;TMPSD_HUMAN;.	P	327;357;362;362;362;362	ENSP00000435813:L327P;ENSP00000434279:L362P;ENSP00000387702:L362P;ENSP00000394114:L362P;ENSP00000436502:L362P	ENSP00000337113:L357P	L	-	2	0	TMPRSS13	117285755	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.917000	0.75782	1.884000	0.54569	0.459000	0.35465	CTC			0.622	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000392318.1		NM_032046	
ARHGEF12	23365	mdanderson.org	37	11	120347433	120347433	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr11:120347433C>T	ENST00000397843.2	+	34	3507	c.3341C>T	c.(3340-3342)gCa>gTa	p.A1114V	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.A1095V|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.A1011V	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1114	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GAACTGGTGGCACAGACAGTT	0.343			T	MLL	AML																																p.A1114V				Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	.			0			c.C3341T												119.0	114.0	115.0					11																	120347433		1868	4110	5978	SO:0001583	missense	23365	exon34			TGGTGGCACAGAC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.3341C>T	11.37:g.120347433C>T	ENSP00000380942:p.Ala1114Val		53	0	0		82	0.06	5	NM_015313	36	0.00	0	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459040	0.96240	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.71103	-0.54;-0.54;-0.54	5.1	5.1	0.69264	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.39759	U	0.001275	D	0.86719	0.6000	M	0.87038	2.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.89017	0.3432	10	0.87932	D	0	-15.885	18.8774	0.92343	0.0:1.0:0.0:0.0	.	1011;1095;1114	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	V	1114;1095;1011	ENSP00000380942:A1114V;ENSP00000349056:A1095V;ENSP00000432984:A1011V	ENSP00000349056:A1095V	A	+	2	0	ARHGEF12	119852643	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.410000	0.80065	2.510000	0.84645	0.563000	0.77884	GCA			0.343	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000388052.1		NM_015313	
CLSTN3	9746	broad.mit.edu	37	12	7281645	7281674	+	5'Flank	DEL	TTCCTGAGGAAGGAACCTGGAGCAGGATCC	TTCCTGAGGAAGGAACCTGGAGCAGGATCC	-	rs148894272|rs6144602|rs552263970		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	TTCCTGAGGAAGGAACCTGGAGCAGGATCC	TTCCTGAGGAAGGAACCTGGAGCAGGATCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr12:7281645_7281674delTTCCTGAGGAAGGAACCTGGAGCAGGATCC	ENST00000266546.6	+	0	0				RP11-273B20.1_ENST00000538062.1_RNA|RBP5_ENST00000266560.3_5'Flank|RP11-273B20.1_ENST00000544657.1_RNA|RBP5_ENST00000542370.1_5'Flank	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3						homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						ACCTTGGCTTTTCCTGAGGAAGGAACCTGGAGCAGGATCCTTCCTGAGGA	0.57														5008	1.0	1.0	1.0	5008	,	,		18442	1.0		1.0	False		,,,				2504	1.0				.													.	RBP5	20		0			.																																									SO:0001631	upstream_gene_variant	0	.			TGGCTTTTCCTGA	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167		12.37:g.7281645_7281674delTTCCTGAGGAAGGAACCTGGAGCAGGATCC	Exception_encountered		6	0	0		12	0.42	5	.	2	0.00	0	D3DUT6|O94831|Q2T9J5|Q5UE57	RNA	DEL	ENST00000266546.6	37	CCDS8575.1																																																																																					0.570	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398560.2		NM_014718	
GRIN2B	2904	broad.mit.edu	37	12	13717472	13717472	+	Silent	SNP	G	G	T	rs531269037		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr12:13717472G>T	ENST00000609686.1	-	13	2909	c.2700C>A	c.(2698-2700)cgC>cgA	p.R900R		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	900					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCGCAGCAGGCGCAGGATGT	0.577																																					p.R900R													GRIN2B,right_upper_lobe,carcinoma,-2,1	GRIN2B	303	1	0			c.C2700A												147.0	135.0	139.0					12																	13717472		2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			CAGCAGGCGCAGG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2700C>A	12.37:g.13717472G>T			95	0	0		136	0.03	4	NM_000834	0		0	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																					0.577	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000268014.2			
RARG	5916	mdanderson.org	37	12	53609159	53609159	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr12:53609159G>T	ENST00000425354.2	-	5	880	c.393C>A	c.(391-393)aaC>aaA	p.N131K	RARG_ENST00000543726.1_Missense_Mutation_p.N109K|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000327550.3_Missense_Mutation_p.N59K|RARG_ENST00000394426.1_Missense_Mutation_p.N131K|RARG_ENST00000338561.5_Missense_Mutation_p.N120K	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	131					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	TGATGATACAGTTTTTGTCGC	0.532																																					p.N131K													.	.			0			c.C393A												260.0	201.0	221.0					12																	53609159		2203	4300	6503	SO:0001583	missense	5916	exon5			GATACAGTTTTTG	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.393C>A	12.37:g.53609159G>T	ENSP00000388510:p.Asn131Lys		114	0.0087719298	1		110	0.05	5	NM_000966	25	0.00	0	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	37	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	G	8.695	0.908346	0.17833	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	D;D;D;D;D	0.96992	-4.02;-4.02;-4.02;-4.02;-4.2	4.45	2.62	0.31277	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.96144	0.8743	L	0.46819	1.47	0.58432	D	0.999995	B;B;D;B	0.67145	0.094;0.449;0.996;0.04	B;B;D;B	0.67382	0.108;0.372;0.951;0.074	D	0.94029	0.7299	10	0.38643	T	0.18	.	9.4511	0.38727	0.177:0.0:0.823:0.0	.	168;109;131;120	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	K	131;131;59;120;109;168	ENSP00000388510:N131K;ENSP00000377947:N131K;ENSP00000332695:N59K;ENSP00000343698:N120K;ENSP00000444335:N109K	ENSP00000332695:N59K	N	-	3	2	RARG	51895426	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	3.321000	0.51999	0.625000	0.30304	-0.218000	0.12543	AAC			0.532	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000109404.2		NM_000966	
LRCOL1	100507055	broad.mit.edu	37	12	133182784	133182786	+	lincRNA	DEL	CAG	CAG	-			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	CAG	CAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr12:133182784_133182786delCAG	ENST00000545517.1	-	0	64_66							A6NCL2	LRCL1_HUMAN	leucine rich colipase-like 1						digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										CCATGGACCCcagcagcagcagc	0.65																																					p.18_18del													.	.			0			c.52_54del																																											100507055	exon2			GGACCCCAGCAGC		CCDS73547.1	12q24.33	2012-07-02			ENSG00000204583	ENSG00000204583			44160	protein-coding gene	gene with protein product							Standard	NM_001195520		Approved		uc021rgr.1	A6NCL2	OTTHUMG00000168043		12.37:g.133182793_133182795delCAG			6	0	0		6	0.33	2	NM_001195520	0		0	H9BFB1	RNA	DEL	ENST00000545517.1	37																																																																																						0.650	LRCOL1-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000397683.1		NM_001195520	
POSTN	10631	mdanderson.org	37	13	38145583	38145583	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr13:38145583G>T	ENST00000379747.4	-	18	2219	c.2102C>A	c.(2101-2103)aCa>aAa	p.T701K	POSTN_ENST00000541481.1_Intron|POSTN_ENST00000379742.4_Intron|POSTN_ENST00000497145.1_5'UTR|POSTN_ENST00000379743.4_Missense_Mutation_p.T674K|POSTN_ENST00000541179.1_Missense_Mutation_p.T674K|POSTN_ENST00000379749.4_Missense_Mutation_p.T701K	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	701					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTTGACTTTTGTTAGTGTGGG	0.368																																					p.T701K													.	.			0			c.C2102A												190.0	169.0	176.0					13																	38145583		2202	4299	6501	SO:0001583	missense	10631	exon18			ACTTTTGTTAGTG	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.2102C>A	13.37:g.38145583G>T	ENSP00000369071:p.Thr701Lys		96	0.0208333333	2		82	0.06	5	NM_006475	207	0.00	0	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	G	7.627	0.677982	0.14841	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743	D;D;D;D	0.94046	-3.29;-3.17;-3.18;-3.34	4.95	3.19	0.36642	.	0.168195	0.52532	D	0.000070	D	0.89729	0.6799	L	0.59436	1.845	0.39419	D	0.966892	B;P;B	0.35575	0.025;0.51;0.012	B;B;B	0.32864	0.016;0.154;0.012	D	0.86610	0.1872	10	0.38643	T	0.18	-3.7446	10.231	0.43256	0.072:0.0:0.7914:0.1366	.	674;674;701	B1ALD8;Q15063-3;Q15063	.;.;POSTN_HUMAN	K	674;701;701;674	ENSP00000437959:T674K;ENSP00000369073:T701K;ENSP00000369071:T701K;ENSP00000369067:T674K	ENSP00000369067:T674K	T	-	2	0	POSTN	37043583	1.000000	0.71417	0.074000	0.20217	0.090000	0.18270	4.408000	0.59761	0.742000	0.32697	-1.078000	0.02229	ACA			0.368	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000044566.2		NM_006475	
RP11-597A11.1	0	broad.mit.edu	37	14	20086237	20086237	+	RNA	DEL	T	T	-	rs569592353|rs373441912	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr14:20086237delT	ENST00000548261.1	+	0	51																											GGTGTGTGTGTGGGGGGGTAT	0.388													|||unknown(STR2?)	915	0.182708	0.2443	0.1686	5008	,	,		35626	0.1429		0.1511	False		,,,				2504	0.183				.													.	.			0			.																																											0	.			TGTGTGTGGGGGG																													14.37:g.20086237delT			7	0	0		9	0.56	5	.	0		0		RNA	DEL	ENST00000548261.1	37																																																																																						0.388	RP11-597A11.1-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000409571.1			
Unknown	0	bcgsc.ca	37	15	22145400	22145401	+	IGR	DNP	GC	GC	TT	rs140569468|rs150450298	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr15:22145400_22145401GC>TT								POTEB (62578 upstream) : MIR5701-2 (11364 downstream)																							AACCACACTGGCCAGAGCCATC	0.455																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	100419006	.			ACACTGGCCAGAG																													15.37:g.22145400_22145401delinsTT			32	0.03125	1		25	0.56	14	.	0		0		RNA	DNP		37																																																																																					0	0.455										
HERC2P10	390561	hgsc.bcm.edu	37	15	31117040	31117040	+	IGR	SNP	C	C	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr15:31117040C>A								AC004460.1 (23449 upstream) : FAN1 (79014 downstream)																							TGTGAAATTACCAAATGGCAG	0.493																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	390561	.			AAATTACCAAATG																													15.37:g.31117040C>A			24	0	0		28	0.46	13	.	0		0		RNA	SNP		37																																																																																					0	0.493										
SQRDL	58472	mdanderson.org	37	15	45980603	45980603	+	Splice_Site	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr15:45980603G>T	ENST00000260324.7	+	8	1502		c.e8+1		SQRDL_ENST00000568606.1_Splice_Site	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)						cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		AACAAAGAAGGTTTGTATGCC	0.343																																					.													.	.			0			c.1116+1G>T												85.0	83.0	84.0					15																	45980603		2198	4297	6495	SO:0001630	splice_region_variant	58472	exon9			AAGAAGGTTTGTA	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.1116+1G>T	15.37:g.45980603G>T			38	0	0		45	0.07	3	NM_001271213	0		0	Q9UQM8	Splice_Site	SNP	ENST00000260324.7	37	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691118	0.48097	.	.	ENSG00000137767	ENST00000260324	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0926	0.89479	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SQRDL	43767895	1.000000	0.71417	1.000000	0.80357	0.444000	0.32077	8.163000	0.89659	2.671000	0.90904	0.655000	0.94253	.			0.343	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254319.2			Intron
MYO5A	4644	hgsc.bcm.edu	37	15	52662553	52662553	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr15:52662553T>C	ENST00000399231.3	-	22	3122	c.2879A>G	c.(2878-2880)gAg>gGg	p.E960G	MYO5A_ENST00000356338.6_Missense_Mutation_p.E960G|MYO5A_ENST00000553916.1_Missense_Mutation_p.E960G|MYO5A_ENST00000358212.6_Missense_Mutation_p.E960G|MYO5A_ENST00000399233.2_Missense_Mutation_p.E960G	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	960					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		TTTCTCAGTCTCAGAGTTGTA	0.398																																					p.E960G													.	.			0			c.A2879G												67.0	65.0	65.0					15																	52662553		1859	4094	5953	SO:0001583	missense	4644	exon22			TCAGTCTCAGAGT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.2879A>G	15.37:g.52662553T>C	ENSP00000382177:p.Glu960Gly		101	0	0		95	0.04	4	NM_000259	10	0.00	0	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.639429	0.87760	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.52725	0.1752	L	0.58810	1.83	0.80722	D	1	B;D	0.89917	0.226;1.0	B;D	0.85130	0.214;0.997	T	0.52041	-0.8628	10	0.52906	T	0.07	.	15.9526	0.79855	0.0:0.0:0.0:1.0	.	960;960	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	G	960;494;960;960;960;590;960	ENSP00000382177:E960G;ENSP00000382179:E960G;ENSP00000348693:E960G;ENSP00000350945:E960G;ENSP00000451109:E960G	ENSP00000348693:E960G	E	-	2	0	MYO5A	50449845	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.162000	0.77515	2.168000	0.68352	0.533000	0.62120	GAG			0.398	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000268102.1		NM_000259	
ABCC6	368	ucsc.edu;bcgsc.ca	37	16	16251629	16251629	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr16:16251629G>T	ENST00000205557.7	-	27	3802	c.3773C>A	c.(3772-3774)cCc>cAc	p.P1258H		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1258					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CTGAGGCCAGGGGGGCTGAGC	0.622																																					p.P1258H													.	ABCC6	110		0			c.C3773A												36.0	33.0	34.0					16																	16251629		2197	4300	6497	SO:0001583	missense	368	exon27			GGCCAGGGGGGCT	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3773C>A	16.37:g.16251629G>T	ENSP00000205557:p.Pro1258His		40	0	0		39	0.10	4	NM_001171	3	0.00	0	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	g	13.37	2.218118	0.39201	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.90563	-2.69	5.15	3.16	0.36331	.	1.205650	0.06301	U	0.700947	D	0.86883	0.6040	L	0.31845	0.965	0.58432	D	0.999999	D	0.54047	0.964	B	0.43701	0.428	T	0.76405	-0.2971	10	0.48119	T	0.1	.	8.949	0.35776	0.2592:0.0:0.7408:0.0	.	1258	O95255	MRP6_HUMAN	H	1258;196	ENSP00000205557:P1258H	ENSP00000205557:P1258H	P	-	2	0	ABCC6	16159130	0.995000	0.38212	0.511000	0.27724	0.536000	0.34869	0.975000	0.29449	0.562000	0.29204	-0.293000	0.09583	CCC			0.622	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252232.2			
RLTPR	146206	mdanderson.org	37	16	67683413	67683413	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr16:67683413G>T	ENST00000334583.6	+	20	2138	c.1810G>T	c.(1810-1812)Gcc>Tcc	p.A604S	RLTPR_ENST00000545661.1_Missense_Mutation_p.A568S	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	604	Tropomodulin-like.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CCTACTCCGGGCCCTAGCCAC	0.627																																					p.A604S													.	.			0			c.G1810T												39.0	44.0	43.0					16																	67683413		2019	4177	6196	SO:0001583	missense	146206	exon20			CTCCGGGCCCTAG	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1810G>T	16.37:g.67683413G>T	ENSP00000334958:p.Ala604Ser		30	0	0		18	0.11	2	NM_001013838	14	0.00	0	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	37	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.717676	0.89205	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.56275	0.47;0.47	5.09	5.09	0.68999	.	0.129409	0.51477	D	0.000087	T	0.65460	0.2693	M	0.86502	2.82	0.43238	D	0.995149	P;P	0.52463	0.953;0.911	P;B	0.46940	0.532;0.432	T	0.70521	-0.4849	10	0.34782	T	0.22	-21.2483	18.1015	0.89507	0.0:0.0:1.0:0.0	.	568;604	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	S	604;568	ENSP00000334958:A604S;ENSP00000441481:A568S	ENSP00000334958:A604S	A	+	1	0	RLTPR	66240914	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.682000	0.84083	2.390000	0.81377	0.561000	0.74099	GCC			0.627	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000467858.1		NM_001013838	
RANBP10	57610	mdanderson.org	37	16	67763875	67763875	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr16:67763875G>T	ENST00000317506.3	-	8	1079	c.964C>A	c.(964-966)Ctg>Atg	p.L322M	RANBP10_ENST00000411657.2_Missense_Mutation_p.L205M|RANBP10_ENST00000536251.1_Missense_Mutation_p.L93M|RANBP10_ENST00000602677.1_Missense_Mutation_p.L322M|RANBP10_ENST00000448631.2_Missense_Mutation_p.L266M	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	322	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		TTGTGCTCCAGCAGCCCTGGG	0.622																																					p.L322M													.	.			0			c.C964A												100.0	88.0	92.0					16																	67763875		2198	4300	6498	SO:0001583	missense	57610	exon8			GCTCCAGCAGCCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.964C>A	16.37:g.67763875G>T	ENSP00000316589:p.Leu322Met		57	0	0		46	0.07	3	NM_020850	32	0.00	0	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	37	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.842358	0.71488	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000536251;ENST00000411657	.	.	.	6.07	4.13	0.48395	CTLH, C-terminal LisH motif (2);	0.000000	0.85682	D	0.000000	T	0.80221	0.4583	M	0.88775	2.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.99	D;D;P	0.91635	0.999;0.999;0.903	T	0.83037	-0.0159	9	0.72032	D	0.01	-9.7963	10.5149	0.44883	0.1491:0.0:0.8509:0.0	.	205;266;322	B4DID0;B4DQH9;Q6VN20	.;.;RBP10_HUMAN	M	322;266;93;205	.	ENSP00000316589:L322M	L	-	1	2	RANBP10	66321376	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.921000	0.48852	1.585000	0.49928	0.655000	0.94253	CTG			0.622	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000467896.1		NM_020850	
RP11-252A24.2	0	broad.mit.edu	37	16	74372765	74372765	+	RNA	SNP	T	T	C	rs2549261	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr16:74372765T>C	ENST00000429810.2	-	0	1431																											GAAGTCCCAGTGGGGAACCTT	0.502													.|||	41	0.0081869	0.0053	0.0029	5008	,	,		17977	0.0099		0.0139	False		,,,				2504	0.0082				.													.	.			0			.																																											0	.			TCCCAGTGGGGAA																													16.37:g.74372765T>C			79	0.0126582278	1		107	0.07	7	.	13	0.00	0		RNA	SNP	ENST00000429810.2	37																																																																																						0.502	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene		OTTHUMT00000434683.1			
ANKFY1	51479	mdanderson.org	37	17	4071123	4071123	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:4071123G>A	ENST00000341657.4	-	25	3495	c.3460C>T	c.(3460-3462)Cgg>Tgg	p.R1154W	ANKFY1_ENST00000574367.1_Missense_Mutation_p.R1155W|CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000570535.1_Missense_Mutation_p.R1196W	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	1154					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						TTGCAAACCCGCACAGGCTTG	0.512																																					p.R1196W													.	.			0			c.C3586T												59.0	64.0	63.0					17																	4071123		1876	4105	5981	SO:0001583	missense	51479	exon25			AAACCCGCACAGG	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.3460C>T	17.37:g.4071123G>A	ENSP00000343362:p.Arg1154Trp		90	0	0		80	0.05	4	NM_001257999	46	0.00	0	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	19.72	3.879987	0.72294	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	4.88	3.89	0.44902	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.91009	0.7172	H	0.99746	4.745	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;0.999;0.999	D	0.94446	0.7663	9	0.87932	D	0	-8.4503	13.9789	0.64291	0.0:0.0:0.8473:0.1527	.	1096;1154;1155;1196	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	W	1155;1096	.	ENSP00000343362:R1155W	R	-	1	2	ANKFY1	4017872	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	3.331000	0.52075	1.393000	0.46605	0.563000	0.77884	CGG			0.512	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000438702.1		NM_016376	
SENP3	26168	mdanderson.org	37	17	7466636	7466636	+	Silent	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:7466636G>A	ENST00000429205.2	+	2	292	c.243G>A	c.(241-243)gaG>gaA	p.E81E	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.E81E|SENP3-EIF4A1_ENST00000579777.1_RNA			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	81	Glu-rich.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				aggaagaagaggaggaggagg	0.622																																					p.E81E													.	.			0			c.G243A																																									SO:0001819	synonymous_variant	26168	exon2			AGAAGAGGAGGAG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.243G>A	17.37:g.7466636G>A			123	0	0		123	0.04	5	NM_015670	127	0.00	0	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																						0.622	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				NM_015670	
COX10-AS1	100874058	broad.mit.edu	37	17	13928102	13928102	+	RNA	SNP	C	C	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:13928102C>A	ENST00000602743.1	-	0	224									COX10 antisense RNA 1																		GGTGAGGTGGCCTGCAGCCTG	0.547																																					.													.	.			0			.																																											0	.			AGGTGGCCTGCAG			17p12	2013-05-22	2012-08-15	2010-11-25	ENSG00000236088	ENSG00000236088		"""Long non-coding RNAs"""	38873	non-coding RNA	RNA, long non-coding			"""COX10 antisense RNA (non-protein coding)"", ""COX10 antisense RNA 1 (non-protein coding)"""	COX10AS, COX10-AS			Standard	NR_049718		Approved		uc002goe.1		OTTHUMG00000058771		17.37:g.13928102C>A			469	0.0042643923	2		459	0.01	6	.	1	0.00	0		RNA	SNP	ENST00000602743.1	37																																																																																						0.547	COX10-AS1-005	KNOWN	basic	antisense	processed_transcript		OTTHUMT00000467585.1			
RAB11FIP4	84440	mdanderson.org	37	17	29761077	29761077	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:29761077G>T	ENST00000325874.8	+	3	502	c.273G>T	c.(271-273)gtG>gtT	p.V91V		NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	91	Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.?(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				TGAAGGATGTGCTGTCGGTGG	0.652																																					p.V91V													.	.			1	Unknown(1)	autonomic_ganglia(1)	c.G273T												70.0	59.0	63.0					17																	29761077		2201	4299	6500	SO:0001819	synonymous_variant	84440	exon3			GGATGTGCTGTCG	AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.273G>T	17.37:g.29761077G>T			17	0	0		20	0.10	2	NM_032932	7	0.00	0	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																					0.652	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256195.2		NM_032932	
MED1	5469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	37604156	37604156	+	Splice_Site	SNP	C	C	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:37604156C>G	ENST00000394287.3	-	2	232	c.27G>C	c.(25-27)gaG>gaC	p.E9D	MED1_ENST00000300651.6_Splice_Site_p.E9D			O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GCTTTTCTGACTCTATGATTT	0.383										HNSCC(31;0.082)																											p.E9D	Pancreas(21;279 768 2492 4877 24026)												.	.			0			c.G27C												109.0	99.0	103.0					17																	37604156		2203	4300	6503	SO:0001630	splice_region_variant	5469	exon2			TTCTGACTCTATG	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.26-1G>C	17.37:g.37604156C>G			58	0	0		121	0.33	40	NM_004774	28	0.36	10	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000394287.3	37		.	.	.	.	.	.	.	.	.	.	C	10.59	1.391491	0.25118	.	.	ENSG00000125686	ENST00000394287;ENST00000300651	T	0.32753	1.44	5.65	0.13	0.14746	.	.	.	.	.	T	0.28499	0.0705	N	0.24115	0.695	0.34211	D	0.674303	B;B	0.32829	0.267;0.386	P;P	0.54924	0.585;0.764	T	0.48681	-0.9014	9	0.12430	T	0.62	.	2.0223	0.03512	0.1265:0.4726:0.1227:0.2783	.	9;9	Q15648;Q15648-3	MED1_HUMAN;.	D	9	ENSP00000300651:E9D	ENSP00000300651:E9D	E	-	3	2	MED1	34857682	0.181000	0.23161	0.992000	0.48379	0.465000	0.32709	-0.397000	0.07269	-0.144000	0.11314	0.558000	0.71614	GAG			0.383	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000256944.1		NM_004774	Missense_Mutation
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	A	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:62968690A>G	ENST00000430983.1	-	0	1554					NR_026903.1				archaelysin family metallopeptidase 2 pseudogene 1																		AAAATTCCACAAGTCTCTTGG	0.373																																					.													.	.			0			.																																											0	.			TTCCACAAGTCTC	AK056627		17q24.1	2012-10-16	2010-04-08		ENSG00000214174	ENSG00000214174			26491	pseudogene	pseudogene							Standard	NR_026903		Approved	FLJ32065	uc002jfb.3		OTTHUMG00000132075		17.37:g.62968690A>G			66	0	0		108	0.04	4	.	57	0.00	0		RNA	SNP	ENST00000430983.1	37																																																																																						0.373	AMZ2P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000255102.1		NM_153032	
UNC13D	201294	broad.mit.edu	37	17	73824882	73824882	+	Missense_Mutation	SNP	T	T	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:73824882T>G	ENST00000207549.4	-	31	3516	c.3137A>C	c.(3136-3138)tAc>tCc	p.Y1046S	UNC13D_ENST00000412096.2_Missense_Mutation_p.Y1046S	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	1046					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGTGCGGGGTACGTGAGGGG	0.701									Familial Hemophagocytic Lymphohistiocytosis																												p.Y1046S													.	UNC13D	68		0			c.A3137C												6.0	7.0	6.0					17																	73824882		2087	4136	6223	SO:0001583	missense	201294	exon31	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCGGGGTACGTGA	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.3137A>C	17.37:g.73824882T>G	ENSP00000207549:p.Tyr1046Ser		51	0.0980392157	5		36	0.22	8	NM_199242	14	0.00	0	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.143639	0.57044	.	.	ENSG00000092929	ENST00000207549;ENST00000412096	T;T	0.68624	-0.32;-0.34	5.65	4.57	0.56435	.	0.074496	0.53938	D	0.000041	T	0.56156	0.1966	L	0.44542	1.39	0.45607	D	0.998548	B	0.19817	0.039	B	0.18871	0.023	T	0.52518	-0.8565	10	0.27785	T	0.31	-13.2853	11.3216	0.49426	0.0:0.0711:0.0:0.9289	.	1046	Q70J99	UN13D_HUMAN	S	1046	ENSP00000207549:Y1046S;ENSP00000388093:Y1046S	ENSP00000207549:Y1046S	Y	-	2	0	UNC13D	71336477	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.799000	0.69101	2.279000	0.76181	0.533000	0.62120	TAC			0.701	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000448847.2		XM_113950	
CBX4	8535	bcgsc.ca	37	17	77809480	77809481	+	Frame_Shift_Ins	INS	-	-	CCGATATC	rs73422118	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr17:77809480_77809481insCCGATATC	ENST00000269397.4	-	4	387_388	c.210_211insGATATCGG	c.(208-213)cggaagfs	p.K71fs	CBX4_ENST00000448310.1_3'UTR	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	71	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGCCCTCTCTTCCGATATCCCA	0.639											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K71fs													.	CBX4	40		0			c.211_212insGATATCGG																																									SO:0001589	frameshift_variant	8535	exon4			CTCTCTTCCGATA	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.203_210dupGATATCGG	17.37:g.77809481_77809488dupCCGATATC	ENSP00000269397:p.Lys71fs		73	0	0	1178	45	0.07	3	NM_003655	6	0.00	0	B1PJR7|Q6TPI8|Q96C04	Frame_Shift_Ins	INS	ENST00000269397.4	37	CCDS32758.1																																																																																					0.639	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318007.1		NM_003655	
LAMA3	3909	mdanderson.org	37	18	21393036	21393036	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr18:21393036G>T	ENST00000313654.9	+	14	1998	c.1757G>T	c.(1756-1758)tGt>tTt	p.C586F	LAMA3_ENST00000399516.3_Missense_Mutation_p.C586F	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	586	Domain V.|Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGCAGTGCTTGTGACCCAGCT	0.323																																					p.C586F													.	.			0			c.G1757T												88.0	83.0	85.0					18																	21393036		1823	4072	5895	SO:0001583	missense	3909	exon14			GTGCTTGTGACCC	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1757G>T	18.37:g.21393036G>T	ENSP00000324532:p.Cys586Phe		35	0	0		37	0.08	3	NM_198129	1	0.00	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.414192	0.25465	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.80909	-1.43;-1.43	5.11	5.11	0.69529	EGF-like, laminin (4);	.	.	.	.	D	0.89801	0.6820	H	0.98646	4.29	0.80722	D	1	B;B	0.29481	0.245;0.124	B;B	0.35039	0.194;0.128	D	0.91243	0.5023	9	0.87932	D	0	.	17.0835	0.86604	0.0:0.0:1.0:0.0	.	586;586	Q6VU67;Q16787	.;LAMA3_HUMAN	F	586;586;584	ENSP00000324532:C586F;ENSP00000382432:C586F	ENSP00000324532:C586F	C	+	2	0	LAMA3	19647034	1.000000	0.71417	0.067000	0.19924	0.250000	0.25880	5.712000	0.68407	2.519000	0.84933	0.655000	0.94253	TGT			0.323	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254824.3		NM_000227, NM_198129	
SERPINB8	5271	mdanderson.org	37	18	61649058	61649058	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr18:61649058C>T	ENST00000397985.2	+	4	666	c.410C>T	c.(409-411)gCa>gTa	p.A137V	SERPINB8_ENST00000353706.2_Missense_Mutation_p.A137V|SERPINB8_ENST00000542677.1_5'UTR|SERPINB8_ENST00000397988.3_Missense_Mutation_p.A137V	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	137					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				GACTGGGTGGCAGAGAAGACT	0.443																																					p.A137V													SERPINB8,NS,carcinoma,+1,1	SERPINB8	1	1	0			c.C410T												188.0	174.0	178.0					18																	61649058		2203	4300	6503	SO:0001583	missense	5271	exon4			GGGTGGCAGAGAA	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.410C>T	18.37:g.61649058C>T	ENSP00000381072:p.Ala137Val		31	0	0		33	0.09	3	NM_198833	2	0.00	0	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.55|11.55	1.672672|1.672672	0.29693|0.29693	.|.	.|.	ENSG00000166401|ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000397988;ENST00000441827|ENST00000295211	D;D;D;D|.	0.85171|.	-1.95;-1.95;-1.95;-1.95|.	5.21|5.21	-0.261|-0.261	0.12963|0.12963	Serpin domain (3);|.	1.716000|.	0.02980|.	N|.	0.145521|.	T|.	0.58452|.	0.2123|.	M|M	0.86651|0.86651	2.83|2.83	0.09310|0.09310	N|N	0.999998|0.999998	B;B|.	0.09022|.	0.002;0.002|.	B;B|.	0.20577|.	0.024;0.03|.	T|.	0.53408|.	-0.8443|.	9|.	.|.	.|.	.|.	.|.	6.5844|6.5844	0.22612|0.22612	0.4344:0.4237:0.0:0.1419|0.4344:0.4237:0.0:0.1419	.|.	137;137|.	P50452;Q8N178|.	SPB8_HUMAN;.|.	V|X	137|79	ENSP00000381072:A137V;ENSP00000331368:A137V;ENSP00000381075:A137V;ENSP00000393456:A137V|.	.|.	A|Q	+|+	2|1	0|0	SERPINB8|SERPINB8	59800038|59800038	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.664000|0.664000	0.39144|0.39144	0.735000|0.735000	0.26115|0.26115	0.034000|0.034000	0.15491|0.15491	0.467000|0.467000	0.42956|0.42956	GCA|CAG			0.443	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000134014.1		NM_001031848	
RTTN	25914	hgsc.bcm.edu	37	18	67755229	67755229	+	Missense_Mutation	SNP	C	C	T	rs75356692	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr18:67755229C>T	ENST00000255674.6	-	31	4584	c.4298G>A	c.(4297-4299)cGg>cAg	p.R1433Q	RTTN_ENST00000437017.1_Missense_Mutation_p.R1433Q|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1433					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				ACATACCTCCCGGCGCACCAT	0.478													C|||	2	0.000399361	0.0	0.0	5008	,	,		17246	0.0		0.002	False		,,,				2504	0.0				p.R1433Q													RTTN,NS,carcinoma,-1,1	RTTN	-1	1	0			c.G4298A							C	GLN/ARG	1,3849		0,1,1924	89.0	88.0	88.0		4298	5.4	1.0	18	dbSNP_131	88	4,8230		0,4,4113	yes	missense	RTTN	NM_173630.3	43	0,5,6037	TT,TC,CC		0.0486,0.026,0.0414	probably-damaging	1433/2227	67755229	5,12079	1925	4117	6042	SO:0001583	missense	25914	exon31			ACCTCCCGGCGCA	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.4298G>A	18.37:g.67755229C>T	ENSP00000255674:p.Arg1433Gln		79	0	0		71	0.04	3	NM_173630	10	0.00	0	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	29.8	5.036776	0.93630	2.6E-4	4.86E-4	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.65549	-0.16;-0.16	5.45	5.45	0.79879	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.79353	0.4431	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77877	-0.2424	10	0.44086	T	0.13	.	19.6539	0.95828	0.0:1.0:0.0:0.0	.	1433	Q86VV8	RTTN_HUMAN	Q	1433	ENSP00000255674:R1433Q;ENSP00000399520:R1433Q	ENSP00000255674:R1433Q	R	-	2	0	RTTN	65906209	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.485000	0.66850	2.719000	0.93026	0.484000	0.47621	CGG	0.001		0.478	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000442988.1		NM_173630	
RFX1	5989	mdanderson.org	37	19	14073848	14073848	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr19:14073848C>T	ENST00000254325.4	-	20	2962	c.2728G>A	c.(2728-2730)Gcc>Acc	p.A910T		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	910	Necessary for dimerization.				immune response (GO:0006955)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			GCCAGATTGGCGAACTGGAGG	0.716																																					p.A910T													.	.			0			c.G2728A												31.0	31.0	31.0					19																	14073848		2012	3976	5988	SO:0001583	missense	5989	exon20			GATTGGCGAACTG		CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 1"", ""enhancer factor C"", ""MHC class II regulatory factor RFX"""	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.2728G>A	19.37:g.14073848C>T	ENSP00000254325:p.Ala910Thr		89	0	0		46	0.07	3	NM_002918	173	0.00	0		Missense_Mutation	SNP	ENST00000254325.4	37	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	c	16.97	3.268460	0.59540	.	.	ENSG00000132005	ENST00000254325	T	0.47177	0.85	5.0	3.94	0.45596	.	0.247552	0.39834	N	0.001259	T	0.34077	0.0885	L	0.47716	1.5	0.45452	D	0.998428	P	0.48694	0.914	B	0.34038	0.174	T	0.12167	-1.0558	10	0.28530	T	0.3	-26.4741	11.8961	0.52658	0.1754:0.8246:0.0:0.0	.	910	P22670	RFX1_HUMAN	T	910	ENSP00000254325:A910T	ENSP00000254325:A910T	A	-	1	0	RFX1	13934848	1.000000	0.71417	0.992000	0.48379	0.823000	0.46562	2.353000	0.44089	1.081000	0.41110	0.416000	0.27883	GCC			0.716	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000458510.1		NM_002918	
LPHN1	22859	mdanderson.org	37	19	14262420	14262420	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr19:14262420G>T	ENST00000340736.6	-	24	3987	c.3690C>A	c.(3688-3690)ccC>ccA	p.P1230P	CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Silent_p.P1225P|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1230					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGCCTCCCAAGGGGTGCTCTG	0.617																																					p.P1230P													.	.			0			c.C3690A												51.0	58.0	56.0					19																	14262420		1956	4027	5983	SO:0001819	synonymous_variant	22859	exon24			TCCCAAGGGGTGC	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.3690C>A	19.37:g.14262420G>T			30	0	0		20	0.10	2	NM_001008701	96	0.00	0	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																					0.617	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000459696.1		NM_014921	
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	42796253	42796253	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr19:42796253C>G	ENST00000575354.2	+	12	2942	c.2902C>G	c.(2902-2904)Ccg>Gcg	p.P968A	CIC_ENST00000160740.3_Missense_Mutation_p.P968A|CIC_ENST00000572681.2_Missense_Mutation_p.P1877A	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	968	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCAGCTGACCCCGGTGCCTGT	0.652			"""Mis, F, S"""		oligodendroglioma																																p.P968A				Rec	yes		19	19q13.2	23152	capicua homolog		O	.	.			0			c.C2902G												73.0	80.0	78.0					19																	42796253		2203	4300	6503	SO:0001583	missense	23152	exon12			CTGACCCCGGTGC	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2902C>G	19.37:g.42796253C>G	ENSP00000458663:p.Pro968Ala		128	0	0		67	0.28	19	NM_015125	53	0.38	20	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071537	0.55646	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	T	0.57272	0.2042	L	0.29908	0.895	0.42671	D	0.99351	D	0.55172	0.97	P	0.51833	0.681	T	0.63102	-0.6712	8	0.87932	D	0	-11.2505	15.6181	0.76784	0.0:1.0:0.0:0.0	.	968	Q96RK0	CIC_HUMAN	A	968	.	ENSP00000160740:P968A	P	+	1	0	CIC	47488093	0.986000	0.35501	0.997000	0.53966	0.938000	0.57974	2.794000	0.47853	2.571000	0.86741	0.561000	0.74099	CCG			0.652	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000438532.2			
RASIP1	54922	mdanderson.org	37	19	49224143	49224143	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr19:49224143C>T	ENST00000222145.4	-	12	3008	c.2804G>A	c.(2803-2805)cGt>cAt	p.R935H	MAMSTR_ENST00000318083.6_5'Flank|MAMSTR_ENST00000419611.1_5'Flank|MAMSTR_ENST00000377367.3_5'Flank	NM_017805.2	NP_060275.2	Q5U651	RAIN_HUMAN	Ras interacting protein 1	935					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|negative regulation of autophagy (GO:0010507)|regulation of Rho GTPase activity (GO:0032319)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	Golgi apparatus (GO:0005794)		p.R935P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	21		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)		GCGGAGCCTACGGAGTTCACG	0.642																																					p.R935H													RASIP1,NS,NS,0,1	RASIP1	0	1	1	Substitution - Missense(1)	pancreas(1)	c.G2804A												59.0	59.0	59.0					19																	49224143		2203	4300	6503	SO:0001583	missense	54922	exon12			AGCCTACGGAGTT	BC028614	CCDS12731.1	19q13.33	2008-02-05				ENSG00000105538			24716	protein-coding gene	gene with protein product		609623				15031288	Standard	NM_017805		Approved	FLJ20401, RAIN	uc002pki.3	Q5U651		ENST00000222145.4:c.2804G>A	19.37:g.49224143C>T	ENSP00000222145:p.Arg935His		74	0	0		47	0.06	3	NM_017805	35	0.00	0	Q6U676	Missense_Mutation	SNP	ENST00000222145.4	37	CCDS12731.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867519	0.72065	.	.	ENSG00000105538	ENST00000222145	T	0.23552	1.9	5.58	5.58	0.84498	.	0.252347	0.37906	N	0.001895	T	0.25791	0.0628	L	0.29908	0.895	0.32228	N	0.574381	D	0.69078	0.997	P	0.45660	0.489	T	0.12528	-1.0544	10	0.52906	T	0.07	-10.9615	17.4533	0.87599	0.0:1.0:0.0:0.0	.	935	Q5U651	RAIN_HUMAN	H	935	ENSP00000222145:R935H	ENSP00000222145:R935H	R	-	2	0	RASIP1	53915955	0.924000	0.31332	1.000000	0.80357	0.256000	0.26092	1.808000	0.38912	2.813000	0.96785	0.655000	0.94253	CGT			0.642	RASIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000466185.1		NM_017805	
SSC5D	284297	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	56011494	56011494	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr19:56011494T>C	ENST00000389623.6	+	10	2040	c.2017T>C	c.(2017-2019)Tcc>Ccc	p.S673P	SSC5D_ENST00000587166.1_Missense_Mutation_p.S673P	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	673	Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						CACTGAGGCCTCCCGAAGACC	0.627																																					p.S673P													.	SSC5D	65		0			c.T2017C												109.0	114.0	112.0					19																	56011494		692	1591	2283	SO:0001583	missense	284297	exon10			GAGGCCTCCCGAA		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.2017T>C	19.37:g.56011494T>C	ENSP00000374274:p.Ser673Pro		109	0.0091743119	1		70	0.10	7	NM_001195267	8	0.38	3	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586045	0.46110	.	.	ENSG00000179954	ENST00000389623;ENST00000541230	T	0.01359	4.98	3.34	1.17	0.20885	.	.	.	.	.	T	0.01254	0.0041	L	0.27053	0.805	0.09310	N	1	B	0.17667	0.023	B	0.12156	0.007	T	0.46965	-0.9153	9	0.66056	D	0.02	.	4.645	0.12568	0.0:0.2928:0.0:0.7072	.	673	A1L4H1	SRCRL_HUMAN	P	673	ENSP00000374274:S673P	ENSP00000374274:S673P	S	+	1	0	SSC5D	60703306	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	-0.472000	0.06623	0.313000	0.23062	0.443000	0.29094	TCC			0.627	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000453345.2		XM_001718392	
LPIN1	23175	broad.mit.edu;mdanderson.org	37	2	11945257	11945257	+	Missense_Mutation	SNP	G	G	A	rs147550491		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr2:11945257G>A	ENST00000256720.2	+	16	2209	c.2116G>A	c.(2116-2118)Gct>Act	p.A706T	LPIN1_ENST00000404113.2_Missense_Mutation_p.A207T|LPIN1_ENST00000449576.2_Missense_Mutation_p.A791T|LPIN1_ENST00000396097.1_Missense_Mutation_p.A436T|LPIN1_ENST00000396099.1_Missense_Mutation_p.A748T|LPIN1_ENST00000425416.2_Missense_Mutation_p.A712T	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	706	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TCAGGGCATCGCTAAGCTGTA	0.468																																					p.A791T													.	LPIN1	99		0			c.G2371A							G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	120.0	104.0	110.0		2116	5.2	0.1	2	dbSNP_134	110	0,8600		0,0,4300	no	missense	LPIN1	NM_145693.1	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	706/891	11945257	1,13005	2203	4300	6503	SO:0001583	missense	23175	exon18			GGCATCGCTAAGC	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2116G>A	2.37:g.11945257G>A	ENSP00000256720:p.Ala706Thr		91	0	0		95	0.04	4	NM_001261428	10	0.00	0	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694235	0.88735	2.27E-4	0.0	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.15	5.15	0.70609	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.85682	D	0.000000	D	0.86590	0.5969	M	0.63208	1.945	0.80722	D	1	D;D;D	0.89917	0.99;1.0;0.994	P;D;P	0.91635	0.844;0.999;0.903	D	0.84741	0.0751	10	0.34782	T	0.22	-25.1304	18.9934	0.92803	0.0:0.0:1.0:0.0	.	207;791;706	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	T	791;748;712;706;436;207	ENSP00000397908:A791T;ENSP00000379406:A748T;ENSP00000401522:A712T;ENSP00000256720:A706T;ENSP00000379404:A436T;ENSP00000386120:A207T	ENSP00000256720:A706T	A	+	1	0	LPIN1	11862708	1.000000	0.71417	0.135000	0.22099	0.991000	0.79684	9.284000	0.95882	2.569000	0.86673	0.563000	0.77884	GCT			0.468	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000239296.3		NM_145693	
LHCGR	3973	broad.mit.edu	37	2	48982761	48982761	+	Missense_Mutation	SNP	A	A	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr2:48982761A>T	ENST00000294954.7	-	1	71	c.50T>A	c.(49-51)cTg>cAg	p.L17Q	LHCGR_ENST00000403273.1_Missense_Mutation_p.L17Q|LHCGR_ENST00000401907.1_Missense_Mutation_p.L17Q|LHCGR_ENST00000344775.3_Missense_Mutation_p.L17Q|LHCGR_ENST00000405626.1_Missense_Mutation_p.L17Q|STON1-GTF2A1L_ENST00000402114.2_Intron	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	17					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	cggcggctgcagcagcagcag	0.721																																					p.L17Q													.	LHCGR	154		0			c.T50A												1.0	3.0	2.0					2																	48982761		941	1909	2850	SO:0001583	missense	3973	exon1			GGCTGCAGCAGCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.50T>A	2.37:g.48982761A>T	ENSP00000294954:p.Leu17Gln		31	0	0		27	0.11	3	NM_000233	0		0	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	37	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.403405	0.62288	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626;ENST00000403273;ENST00000401907	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	4.29	-1.16	0.09678	.	0.305275	0.27019	N	0.021324	T	0.53206	0.1782	L	0.29908	0.895	0.09310	N	0.999993	P	0.37864	0.61	B	0.28784	0.094	T	0.46721	-0.9171	9	.	.	.	.	3.9646	0.09426	0.4938:0.1876:0.3185:0.0	.	17	P22888	LSHR_HUMAN	Q	17	ENSP00000344301:L17Q;ENSP00000294954:L17Q;ENSP00000386033:L17Q;ENSP00000385847:L17Q;ENSP00000385406:L17Q	.	L	-	2	0	LHCGR	48836265	0.027000	0.19231	0.867000	0.34043	0.542000	0.35054	-0.055000	0.11807	-0.388000	0.07797	0.421000	0.28195	CTG			0.721	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251364.4		NM_000233.3	
SERPINE2	5270	mdanderson.org	37	2	224866576	224866576	+	Silent	SNP	C	C	T	rs12436	byFrequency	TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr2:224866576C>T	ENST00000258405.4	-	2	284	c.42G>A	c.(40-42)acG>acA	p.T14T	SERPINE2_ENST00000447280.2_Silent_p.T26T|SERPINE2_ENST00000409840.3_Silent_p.T14T|SERPINE2_ENST00000409304.1_Silent_p.T14T	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	14					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGGAAGGCAGCGTCACAGAGG	0.478																																					p.T26T													SERPINE2_ENST00000447280,NS,carcinoma,-1,2	SERPINE2_ENST00000447280	-1	2	0			c.G78A												100.0	112.0	108.0					2																	224866576		2203	4300	6503	SO:0001819	synonymous_variant	5270	exon2			AGGCAGCGTCACA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.42G>A	2.37:g.224866576C>T			59	0	0		45	0.07	3	NM_001136530	279	0.00	0	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																					0.478	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000256865.2		NM_006216	
NCOA6	23054	broad.mit.edu	37	20	33345759	33345759	+	Silent	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr20:33345759C>T	ENST00000374796.2	-	8	3362	c.792G>A	c.(790-792)caG>caA	p.Q264Q	NCOA6_ENST00000359003.2_Silent_p.Q264Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	264	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q264Q(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gttgttgttgctgctgctgct	0.532																																					p.Q264Q													NCOA6,NS,carcinoma,0,1	NCOA6	219	1	1	Substitution - coding silent(1)	endometrium(1)	c.G792A												60.0	52.0	55.0					20																	33345759		2203	4300	6503	SO:0001819	synonymous_variant	23054	exon7			TTGTTGCTGCTGC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.792G>A	20.37:g.33345759C>T			70	0	0		91	0.03	3	NM_014071	12	0.00	0	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																					0.532	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000078811.2		NM_014071	
PTGIS	5740	mdanderson.org	37	20	48166687	48166687	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr20:48166687G>T	ENST00000244043.4	-	2	143	c.114C>A	c.(112-114)ccC>ccA	p.P38P	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	38			P -> L (in allele CYP8A1*2). {ECO:0000269|PubMed:11281454}.		apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	ACCCCAACCAGGGGATGCTGC	0.532																																					p.P38P													.	.			0			c.C114A												81.0	67.0	72.0					20																	48166687		2203	4300	6503	SO:0001819	synonymous_variant	5740	exon2			CAACCAGGGGATG		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.114C>A	20.37:g.48166687G>T			45	0	0		41	0.07	3	NM_000961	22	0.00	0	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																					0.532	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080496.2			
CTCFL	140690	broad.mit.edu	37	20	56094264	56094264	+	Splice_Site	SNP	T	T	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr20:56094264T>C	ENST00000608263.1	-	3	1585	c.924A>G	c.(922-924)acA>acG	p.T308T	CTCFL_ENST00000502686.2_Splice_Site_p.T46T|CTCFL_ENST00000433949.3_Splice_Site_p.T103T|CTCFL_ENST00000422869.2_Splice_Site_p.T308T|CTCFL_ENST00000481655.2_Splice_Site_p.T308T|CTCFL_ENST00000429804.3_Splice_Site_p.T308T|CTCFL_ENST00000608440.1_Splice_Site_p.T308T|CTCFL_ENST00000423479.3_Splice_Site_p.T308T|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Splice_Site_p.T308T|CTCFL_ENST00000608425.1_Splice_Site_p.T308T|CTCFL_ENST00000608158.1_Splice_Site_p.T308T|CTCFL_ENST00000539382.1_Splice_Site_p.T103T|CTCFL_ENST00000432255.2_Splice_Site_p.T308T|CTCFL_ENST00000371196.2_Splice_Site_p.T308T|CTCFL_ENST00000608903.1_Splice_Site_p.T46T|CTCFL_ENST00000609232.1_Splice_Site_p.T308T	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	308					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|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)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CAGTTTTACCTGTGTGGGTGT	0.458																																					p.T308T													.	CTCFL	97		0			c.A924G												76.0	78.0	77.0					20																	56094264		2203	4300	6503	SO:0001630	splice_region_variant	140690	exon3			TTTACCTGTGTGG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.925+1A>G	20.37:g.56094264T>C			135	0	0		161	0.01	2	NM_001269044	0		0	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Splice_Site	SNP	ENST00000608263.1	37	CCDS13459.1																																																																																					0.458	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000472040.1		NM_080618	Silent
GGT3P	2679	broad.mit.edu	37	22	18769697	18769697	+	RNA	SNP	A	A	G	rs370008023		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr22:18769697A>G	ENST00000412448.1	-	0	981							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										GTTTTCCAGGACTGCCGCCAA	0.682																																					.													.	.			0			.																																											0	.			TCCAGGACTGCCG			22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18769697A>G			727	0.0013755158	1		745	0.01	8	.	3	0.00	0		RNA	SNP	ENST00000412448.1	37																																																																																						0.682	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000341281.1		NR_003267	
DGKG	1608	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	185975651	185975651	+	Missense_Mutation	SNP	T	T	C	rs560924252		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr3:185975651T>C	ENST00000265022.3	-	17	2041	c.1502A>G	c.(1501-1503)gAt>gGt	p.D501G	DGKG_ENST00000544847.1_Missense_Mutation_p.D442G|DGKG_ENST00000344484.4_Missense_Mutation_p.D476G|DGKG_ENST00000382164.4_Missense_Mutation_p.D462G	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	501	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	ACCAATGCAATCCAAAATCCA	0.448													T|||	1	0.000199681	0.0	0.0	5008	,	,		20054	0.0		0.0	False		,,,				2504	0.001				p.D501G													.	DGKG	98		0			c.A1502G												126.0	115.0	119.0					3																	185975651		2203	4300	6503	SO:0001583	missense	1608	exon17			ATGCAATCCAAAA	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1502A>G	3.37:g.185975651T>C	ENSP00000265022:p.Asp501Gly		121	0.0165289256	2		137	0.36	50	NM_001346	0		0	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990235	0.74589	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.33	5.33	0.75918	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.56529	0.1991	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.89917	0.968;0.968;1.0;1.0	D;P;D;D	0.76575	0.91;0.89;0.987;0.988	T	0.59016	-0.7533	10	0.72032	D	0.01	.	14.4259	0.67215	0.0:0.0:0.0:1.0	.	442;476;462;501	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	G	501;476;462;442;465	ENSP00000265022:D501G;ENSP00000339777:D476G;ENSP00000371599:D462G;ENSP00000440507:D442G	ENSP00000265022:D501G	D	-	2	0	DGKG	187458345	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.739000	0.84976	2.240000	0.73641	0.533000	0.62120	GAT			0.448	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000344800.3			
POLN	353497	mdanderson.org	37	4	2082736	2082736	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr4:2082736G>T	ENST00000511885.2	-	23	2689	c.2336C>A	c.(2335-2337)gCc>gAc	p.A779D	POLN_ENST00000382865.1_Missense_Mutation_p.A779D			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	779					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			ATGGATCATGGCCAGCTTGCA	0.587								DNA polymerases (catalytic subunits)																													p.A779D													.	.			0			c.C2336A												171.0	159.0	163.0					4																	2082736		2203	4300	6503	SO:0001583	missense	353497	exon21			ATCATGGCCAGCT	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.2336C>A	4.37:g.2082736G>T	ENSP00000435506:p.Ala779Asp		63	0	0		35	0.09	3	NM_181808	0		0	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.26|17.26	3.343954|3.343954	0.61073|0.61073	.|.	.|.	ENSG00000130997|ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313|ENST00000511098	D;D|.	0.97378|.	-4.36;-4.36|.	4.15|4.15	4.15|4.15	0.48705|0.48705	DNA-directed DNA polymerase, family A, palm domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87807|0.87807	0.6270|0.6270	H|H	0.98612|0.98612	4.28|4.28	0.47341|0.47341	D|D	0.999392|0.999392	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.999;1.0|.	D|D	0.91325|0.91325	0.5085|0.5085	10|5	0.87932|.	D|.	0|.	-13.073|-13.073	12.1593|12.1593	0.54096|0.54096	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	470;779|.	E9PE06;Q7Z5Q5|.	.;DPOLN_HUMAN|.	D|T	779;779;470|412	ENSP00000435506:A779D;ENSP00000372316:A779D|.	ENSP00000253313:A470D|.	A|P	-|-	2|1	0|0	POLN|POLN	2052534|2052534	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.579000|0.579000	0.36224|0.36224	6.200000|6.200000	0.72118|0.72118	2.309000|2.309000	0.77851|0.77851	0.561000|0.561000	0.74099|0.74099	GCC|CCA			0.587	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000205684.2		NM_181808	
RGS12	6002	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	3319740	3319740	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr4:3319740C>T	ENST00000344733.5	+	2	2747	c.1843C>T	c.(1843-1845)Ccc>Tcc	p.P615S	RGS12_ENST00000336727.3_Missense_Mutation_p.P615S|RGS12_ENST00000382788.3_Missense_Mutation_p.P615S|RGS12_ENST00000543385.1_Missense_Mutation_p.P615S	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	615					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CATTTTTGGTCCCCATCGAAA	0.582																																					p.P615S													.	RGS12	128		0			c.C1843T												80.0	96.0	91.0					4																	3319740		2203	4300	6503	SO:0001583	missense	6002	exon2			TTTGGTCCCCATC	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.1843C>T	4.37:g.3319740C>T	ENSP00000339381:p.Pro615Ser		257	0.0038910506	1		199	0.24	48	NM_002926	19	0.58	11	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	C	4.833	0.154889	0.09236	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.28255	1.62;1.74;1.74;1.74	4.66	3.82	0.43975	.	0.443067	0.24056	N	0.041941	T	0.23766	0.0575	L	0.51422	1.61	0.80722	D	1	B;B;B	0.21071	0.011;0.03;0.051	B;B;B	0.19946	0.006;0.008;0.027	T	0.04413	-1.0953	10	0.13108	T	0.6	-20.7107	7.7378	0.28825	0.0:0.7479:0.1638:0.0883	.	615;615;615	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	S	615	ENSP00000440566:P615S;ENSP00000339381:P615S;ENSP00000338509:P615S;ENSP00000372238:P615S	ENSP00000338509:P615S	P	+	1	0	RGS12	3289538	0.146000	0.22672	0.720000	0.30636	0.870000	0.49936	1.844000	0.39269	0.975000	0.38392	-0.339000	0.08088	CCC			0.582	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000206602.1		NM_002926	
KLHL2	11275	mdanderson.org	37	4	166220781	166220781	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr4:166220781G>T	ENST00000226725.6	+	8	1153	c.894G>T	c.(892-894)cgG>cgT	p.R298R	KLHL2_ENST00000514860.1_Silent_p.R302R|KLHL2_ENST00000506761.1_Silent_p.R132R|KLHL2_ENST00000538127.1_Silent_p.R210R|KLHL2_ENST00000421009.2_Silent_p.R201R|KLHL2_ENST00000509028.1_3'UTR	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	298					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		TCCGGACCCGGCTGAGGACAC	0.428																																					p.R302R													.	.			0			c.G906T												80.0	82.0	81.0					4																	166220781		2203	4300	6503	SO:0001819	synonymous_variant	11275	exon8			GACCCGGCTGAGG	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.894G>T	4.37:g.166220781G>T			45	0	0		40	0.08	3	NM_001161521	11	0.00	0	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Silent	SNP	ENST00000226725.6	37	CCDS34094.1																																																																																					0.428	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000364439.1			
TRAPPC11	60684	hgsc.bcm.edu;mdanderson.org	37	4	184589238	184589238	+	Silent	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr4:184589238G>A	ENST00000334690.6	+	5	730	c.528G>A	c.(526-528)ccG>ccA	p.P176P	TRAPPC11_ENST00000357207.4_Silent_p.P176P|TRAPPC11_ENST00000511409.1_3'UTR	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	176					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TTGTACTGCCGCACACTGACC	0.378																																					p.P176P													C4orf41,NS,carcinoma,0,1	C4orf41	0	1	0			c.G528A												139.0	138.0	138.0					4																	184589238		2203	4300	6503	SO:0001819	synonymous_variant	60684	exon5			ACTGCCGCACACT		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.528G>A	4.37:g.184589238G>A			78	0.0128205128	1		100	0.05	5	NM_021942	28	0.00	0	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																					0.378	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000361654.2		NM_021942	
CCNO	10309	broad.mit.edu	37	5	54527462	54527462	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr5:54527462A>C	ENST00000282572.4	-	3	950	c.794T>G	c.(793-795)gTg>gGg	p.V265G	RP11-506H20.1_ENST00000506435.1_RNA	NM_021147.3	NP_066970.3	P22674	CCNO_HUMAN	cyclin O	265					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cell cycle (GO:0007049)|cell division (GO:0051301)|cilium assembly (GO:0042384)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)|embryo development (GO:0009790)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	uracil DNA N-glycosylase activity (GO:0004844)			endometrium(1)|lung(3)|skin(1)	5		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			CAGCTCTGCCACCCCCCGCGC	0.667																																					p.V265G													.	CCNO	17		0			c.T794G												23.0	23.0	23.0					5																	54527462		2193	4288	6481	SO:0001583	missense	10309	exon3			TCTGCCACCCCCC	M87499	CCDS34157.1	5q11.2	2010-11-15	2007-07-26	2007-07-26	ENSG00000152669	ENSG00000152669			18576	protein-coding gene	gene with protein product		607752	"""cyclin U"""	CCNU			Standard	NR_125346		Approved	UDG2, FLJ22422, UNG2	uc003jpw.3	P22674	OTTHUMG00000162598	ENST00000282572.4:c.794T>G	5.37:g.54527462A>C	ENSP00000282572:p.Val265Gly		105	0.1523809524	16		105	0.11	12	NM_021147	9	0.11	1	A8K1W5|Q0P6J2|Q9H6B0|Q9UMD5	Missense_Mutation	SNP	ENST00000282572.4	37	CCDS34157.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.208005	0.58343	.	.	ENSG00000152669	ENST00000282572	T	0.44881	0.91	5.31	5.31	0.75309	Cyclin, C-terminal (1);Cyclin-like (3);	0.235963	0.39544	N	0.001337	T	0.57184	0.2036	L	0.46157	1.445	0.80722	D	1	D	0.69078	0.997	D	0.68621	0.959	T	0.60454	-0.7260	10	0.87932	D	0	.	15.2158	0.73264	1.0:0.0:0.0:0.0	.	265	P22674	CCNO_HUMAN	G	265	ENSP00000282572:V265G	ENSP00000282572:V265G	V	-	2	0	CCNO	54563219	1.000000	0.71417	0.994000	0.49952	0.076000	0.17211	6.619000	0.74219	2.139000	0.66308	0.402000	0.26972	GTG			0.667	CCNO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000369707.1		NM_021147	
TCERG1	10915	broad.mit.edu	37	5	145836872	145836872	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr5:145836872G>T	ENST00000296702.5	+	3	450	c.412G>T	c.(412-414)Gtt>Ttt	p.V138F	TCERG1_ENST00000394421.2_Missense_Mutation_p.V138F	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	138	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAGATATGGGTTGAAAATAA	0.433																																					p.V138F													.	TCERG1	148		0			c.G412T												56.0	55.0	55.0					5																	145836872		2203	4300	6503	SO:0001583	missense	10915	exon3			ATATGGGTTGAAA	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.412G>T	5.37:g.145836872G>T	ENSP00000296702:p.Val138Phe		87	0	0		128	0.04	5	NM_006706	73	0.00	0	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980678	0.74474	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	D;D	0.83419	-1.72;-1.72	5.28	5.28	0.74379	WW/Rsp5/WWP (5);	0.000000	0.85682	D	0.000000	D	0.92506	0.7620	M	0.87617	2.895	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.996	D;D;D	0.85130	0.997;0.98;0.988	D	0.93520	0.6860	10	0.72032	D	0.01	-16.6096	18.9097	0.92477	0.0:0.0:1.0:0.0	.	138;138;138	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	F	138	ENSP00000296702:V138F;ENSP00000377943:V138F	ENSP00000296702:V138F	V	+	1	0	TCERG1	145817065	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.463000	0.83235	0.491000	0.48974	GTT			0.433	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000251886.1		NM_001040006	
TUBB	203068	mdanderson.org	37	6	30691668	30691668	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr6:30691668G>T	ENST00000327892.8	+	4	1135	c.829G>T	c.(829-831)Gga>Tga	p.G277*	TUBB_ENST00000396389.1_Nonsense_Mutation_p.G259*|TUBB_ENST00000396384.1_Nonsense_Mutation_p.G205*|XXbac-BPG252P9.9_ENST00000607476.1_RNA|TUBB_ENST00000330914.3_Nonsense_Mutation_p.G205*|TUBB_ENST00000435534.1_Intron	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	277					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G277*(1)		breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	CACCAGCCGTGGAAGCCAGCA	0.587																																					p.G277X													TUBB,NS,carcinoma,0,1	TUBB	0	1	1	Substitution - Nonsense(1)	lung(1)	c.G829T												66.0	62.0	63.0					6																	30691668		2203	4300	6503	SO:0001587	stop_gained	203068	exon4			AGCCGTGGAAGCC	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"""Tubulins"""	20778	protein-coding gene	gene with protein product	"""class I beta-tubulin"", ""beta1-tubulin"""	191130	"""tubulin, beta polypeptide"", ""tubulin, beta"""			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.829G>T	6.37:g.30691668G>T	ENSP00000339001:p.Gly277*		62	0	0		50	0.06	3	NM_178014	6607	0.00	5	P05218|Q8WUC1|Q9CY33	Nonsense_Mutation	SNP	ENST00000327892.8	37	CCDS4687.1	.	.	.	.	.	.	.	.	.	.	G	38	7.251778	0.98164	.	.	ENSG00000196230	ENST00000327892;ENST00000422827;ENST00000330914;ENST00000396389;ENST00000396384;ENST00000538863	.	.	.	4.25	4.25	0.50352	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.1681	0.65490	0.0:0.0:1.0:0.0	.	.	.	.	X	277;186;205;259;205;131	.	ENSP00000339001:G277X	G	+	1	0	TUBB	30799647	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.301000	0.96167	2.204000	0.70986	0.591000	0.81541	GGA			0.587	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076074.2		NM_178014	
INTS1	26173	broad.mit.edu	37	7	1527082	1527082	+	Silent	SNP	C	C	G			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:1527082C>G	ENST00000404767.3	-	20	2605	c.2520G>C	c.(2518-2520)ggG>ggC	p.G840G	INTS1_ENST00000389470.4_Silent_p.G983G	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	840					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TCCGGGGGGGCCCCCTGAGGG	0.677																																					p.G840G													.	INTS1	145		0			c.G2520C																																									SO:0001819	synonymous_variant	26173	exon20			GGGGGGCCCCCTG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.2520G>C	7.37:g.1527082C>G			104	0.0192307692	2		121	0.04	5	NM_001080453	126	0.02	2	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																					0.677	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000323683.1			
FKBP14	55033	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	30058694	30058696	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	AGG	AGG					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:30058694_30058696delAGG	ENST00000222803.5	-	3	568_570	c.393_395delCCT	c.(391-396)ctcctg>ctg	p.131_132LL>L	AC007285.6_ENST00000422239.1_RNA|AC007285.6_ENST00000419103.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	131	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						TCGAATCTCCAGGAGATCAATAT	0.369																																					p.132_132del													.	FKBP14	18		0			c.394_396del																																									SO:0001651	inframe_deletion	55033	exon3			ATCTCCAGGAGAT	AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"""EF-hand domain containing"""	18625	protein-coding gene	gene with protein product		614505	"""FK506 binding protein 14 (22 kDa)"""			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.393_395delCCT	7.37:g.30058694_30058696delAGG	ENSP00000222803:p.Leu132del		65	0	0		157	0.15	24	NM_017946	59	0.00	0		In_Frame_Del	DEL	ENST00000222803.5	37	CCDS5423.1																																																																																					0.369	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000214229.1		NM_017946	
NCF1	653361	mdanderson.org	37	7	74202921	74202921	+	Silent	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:74202921G>A	ENST00000289473.4	+	10	994	c.924G>A	c.(922-924)gcG>gcA	p.A308A		NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	308	Arg/Lys-rich (highly basic).		A -> V (in dbSNP:rs13739).		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)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	TCCGCAACGCGCACAGCATCC	0.726																																					p.A308A													.	.			0			c.G924A												7.0	7.0	7.0					7																	74202921		2092	4095	6187	SO:0001819	synonymous_variant	653361	exon10			CAACGCGCACAGC	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.924G>A	7.37:g.74202921G>A			57	0	0		35	0.09	3	NM_000265	4	0.00	0	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Silent	SNP	ENST00000289473.4	37	CCDS34657.1																																																																																					0.726	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000314560.1		NM_000265	
CTTNBP2	83992	bcgsc.ca	37	7	117407171	117407171	+	Silent	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:117407171G>A	ENST00000160373.3	-	9	2929	c.2838C>T	c.(2836-2838)tgC>tgT	p.C946C		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	946					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CAGTCCGATTGCACTTGTCTC	0.448																																					p.C946C													.	CTTNBP2	200		0			c.C2838T												185.0	154.0	165.0					7																	117407171		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon9			CCGATTGCACTTG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2838C>T	7.37:g.117407171G>A			58	0	0		53	0.08	4	NM_033427	4	0.00	0	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.258953	0.23051	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.49	2.65	0.31530	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.4675	9.5342	0.39213	0.3134:0.0:0.6866:0.0	.	.	.	.	X	434	.	.	Q	-	1	0	CTTNBP2	117194407	1.000000	0.71417	0.986000	0.45419	0.993000	0.82548	1.337000	0.33862	0.344000	0.23847	0.561000	0.74099	CAA			0.448	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000059201.4		NM_033427	
RP11-274B21.1	0	broad.mit.edu	37	7	128217802	128217803	+	RNA	INS	-	-	GGGAGA	rs139428807		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:128217802_128217803insGGGAGA	ENST00000605862.1	+	0	261																											gagggagaagggggagagggag	0.559																																					.													.	.			0			.																																											0	.			GAGAAGGGGGAGA																													7.37:g.128217803_128217808dupGGGAGA			4	0	0		7	0.43	3	.	0		0		RNA	INS	ENST00000605862.1	37																																																																																						0.559	RP11-274B21.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000468355.1			
CNTNAP2	26047	hgsc.bcm.edu	37	7	148028714	148028714	+	Intron	SNP	C	C	G	rs62470610		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:148028714C>G	ENST00000361727.3	+	22	3991				CNTNAP2_ENST00000538075.1_Intron	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2						adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			cggatggagtcgatggatgga	0.537										HNSCC(39;0.1)																											.													.	.			0			.																																									SO:0001627	intron_variant	100422849	.			TGGAGTCGATGGA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3476-52027C>G	7.37:g.148028714C>G			11	0	0		8	0.63	5	.	0		0	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	RNA	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																					0.537	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000327668.1			
CNTNAP2	26047	ucsc.edu	37	7	148112542	148112542	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:148112542G>A	ENST00000361727.3	+	24	4346	c.3830G>A	c.(3829-3831)tGc>tAc	p.C1277Y	CNTNAP2_ENST00000538075.1_Missense_Mutation_p.C336Y|CNTNAP2_ENST00000463592.2_3'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1277					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ACCATCCTGTGCACCCTGGTC	0.597										HNSCC(39;0.1)																											p.C1277Y													.	CNTNAP2	392		0			c.G3830A												89.0	70.0	77.0					7																	148112542		2203	4300	6503	SO:0001583	missense	26047	exon24			TCCTGTGCACCCT	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3830G>A	7.37:g.148112542G>A	ENSP00000354778:p.Cys1277Tyr		53	0	0		31	0.13	4	NM_014141	20	0.00	0	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509298	0.85282	.	.	ENSG00000174469	ENST00000361727;ENST00000538075	T;T	0.75050	-0.9;-0.9	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.86912	0.6047	M	0.84219	2.685	0.80722	D	1	D	0.76494	0.999	D	0.67103	0.949	D	0.88581	0.3136	10	0.72032	D	0.01	.	17.8137	0.88624	0.0:0.0:1.0:0.0	.	1277	Q9UHC6	CNTP2_HUMAN	Y	1277;336	ENSP00000354778:C1277Y;ENSP00000440732:C336Y	ENSP00000354778:C1277Y	C	+	2	0	CNTNAP2	147743475	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.697000	0.98697	2.534000	0.85438	0.655000	0.94253	TGC			0.597	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000327668.1			
TMEM176B	28959	ucsc.edu	37	7	150489162	150489162	+	Silent	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr7:150489162G>T	ENST00000447204.2	-	6	1074	c.702C>A	c.(700-702)ggC>ggA	p.G234G	TMEM176B_ENST00000450753.2_Silent_p.G197G|TMEM176B_ENST00000492607.1_Silent_p.G234G|TMEM176B_ENST00000434545.1_Silent_p.G234G|TMEM176B_ENST00000326442.5_Silent_p.G234G|TMEM176B_ENST00000429904.2_Silent_p.G234G	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	234					cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGAGCTCTGGCCACACAAGT	0.597																																					p.G234G													.	TMEM176B	36		0			c.C702A												122.0	101.0	108.0					7																	150489162		2203	4300	6503	SO:0001819	synonymous_variant	28959	exon6			GCTCTGGCCACAC	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.702C>A	7.37:g.150489162G>T			62	0	0		37	0.11	4	NM_014020	60	0.00	0	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Silent	SNP	ENST00000447204.2	37	CCDS5908.1																																																																																					0.597	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000349204.1		NM_014020	
ZFHX4	79776	broad.mit.edu	37	8	77617508	77617508	+	Silent	SNP	G	G	A	rs368515394		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr8:77617508G>A	ENST00000521891.2	+	2	1633	c.1185G>A	c.(1183-1185)ccG>ccA	p.P395P	ZFHX4_ENST00000050961.6_Silent_p.P395P|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Silent_p.P395P|ZFHX4_ENST00000518282.1_Silent_p.P395P	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAGAGCAGCCGCTGGGGATTA	0.517										HNSCC(33;0.089)			G|||	1	0.000199681	0.0008	0.0	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.P395P													ZFHX4,NS,carcinoma,0,2	ZFHX4	878	2	0			c.G1185A							G		5,3707		0,5,1851	31.0	31.0	31.0		1185	1.4	1.0	8		31	0,8202		0,0,4101	no	coding-synonymous	ZFHX4	NM_024721.4		0,5,5952	AA,AG,GG		0.0,0.1347,0.042		395/3617	77617508	5,11909	1856	4101	5957	SO:0001819	synonymous_variant	79776	exon2			GCAGCCGCTGGGG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1185G>A	8.37:g.77617508G>A			76	0.0263157895	2		111	0.03	3	NM_024721	3	0.00	0	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																					0.517	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000379197.2		NM_024721	
COL14A1	7373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	121220569	121220569	+	Silent	SNP	T	T	C			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr8:121220569T>C	ENST00000297848.3	+	11	1560	c.1290T>C	c.(1288-1290)gcT>gcC	p.A430A	COL14A1_ENST00000309791.4_Silent_p.A430A|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Silent_p.A335A|COL14A1_ENST00000537875.1_Silent_p.A430A	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CCCACACTGCTAGTGAAGGCC	0.408																																					p.A430A													.	.			0			c.T1290C												98.0	90.0	93.0					8																	121220569		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon11			CACTGCTAGTGAA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1290T>C	8.37:g.121220569T>C			45	0	0		88	0.15	13	NM_021110	74	0.20	15		Silent	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251489	0.22880	.	.	ENSG00000187955	ENST00000523142	.	.	.	5.01	-0.599	0.11645	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8253	0.18550	0.1381:0.4583:0.0:0.4036	.	.	.	.	Q	187	.	.	X	+	1	0	COL14A1	121289750	0.078000	0.21339	0.998000	0.56505	0.966000	0.64601	-0.857000	0.04286	0.034000	0.15491	-0.441000	0.05720	TAG			0.408	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000313657.2		NM_021110	
OPLAH	26873	broad.mit.edu	37	8	145108284	145108284	+	Missense_Mutation	SNP	G	G	T	rs186909122		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr8:145108284G>T	ENST00000426825.1	-	20	2780	c.2699C>A	c.(2698-2700)gCc>gAc	p.A900D	OPLAH_ENST00000534424.1_5'UTR|CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	900					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGCCCGCAGGGCCTCCGTCAC	0.647																																					p.A900D													.	OPLAH	78		0			c.C2699A												44.0	52.0	50.0					8																	145108284		2081	4210	6291	SO:0001583	missense	26873	exon20			CGCAGGGCCTCCG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.2699C>A	8.37:g.145108284G>T	ENSP00000475943:p.Ala900Asp		74	0.0135135135	1		89	0.07	6	NM_017570	13	0.00	0	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	G	14.54	2.564475	0.45694	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.56	3.44	0.39384	.	0.106428	0.64402	D	0.000007	T	0.48132	0.1483	.	.	.	0.52099	D	0.999941	B	0.18863	0.031	B	0.25405	0.06	T	0.61317	-0.7087	7	0.62326	D	0.03	.	10.7882	0.46417	0.1156:0.0:0.8844:0.0	.	900	O14841	OPLA_HUMAN	D	900	.	ENSP00000412071:A900D	A	-	2	0	OPLAH	145180272	1.000000	0.71417	0.999000	0.59377	0.867000	0.49689	3.294000	0.51787	2.069000	0.61940	0.448000	0.29417	GCC			0.647	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_017570	
FAM120A	23196	mdanderson.org	37	9	96214208	96214208	+	Missense_Mutation	SNP	A	A	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:96214208A>T	ENST00000277165.6	+	1	205	c.11A>T	c.(10-12)cAg>cTg	p.Q4L	FAM120A_ENST00000340893.4_Missense_Mutation_p.Q4L|FAM120A_ENST00000333936.5_Missense_Mutation_p.Q4L|FAM120A_ENST00000375389.3_Missense_Mutation_p.Q4L|FAM120AOS_ENST00000423591.1_5'Flank|FAM120AOS_ENST00000375412.5_Intron|FAM120AOS_ENST00000479094.1_5'Flank	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	4						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ATGGGCGTGCAGGGCTTCCAG	0.821																																					p.Q4L													.	.			0			c.A11T												1.0	1.0	1.0					9																	96214208		706	1724	2430	SO:0001583	missense	23196	exon1			GCGTGCAGGGCTT	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.11A>T	9.37:g.96214208A>T	ENSP00000277165:p.Gln4Leu		37	0	0		14	0.21	3	NM_014612	2	0.00	0	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898533	0.72639	.	.	ENSG00000048828	ENST00000375389;ENST00000277165;ENST00000333936;ENST00000340893	T;T;T;T	0.53857	0.6;1.24;1.22;1.25	2.76	1.57	0.23409	.	0.000000	0.37012	U	0.002295	T	0.62356	0.2421	L	0.59436	1.845	0.46631	D	0.999134	P;B	0.51449	0.945;0.13	D;B	0.67900	0.954;0.075	T	0.59968	-0.7354	10	0.87932	D	0	.	7.3255	0.26553	0.8834:0.0:0.1165:0.0	.	4;4	Q9NZB2;Q9NZB2-2	F120A_HUMAN;.	L	4	ENSP00000364538:Q4L;ENSP00000277165:Q4L;ENSP00000334918:Q4L;ENSP00000344698:Q4L	ENSP00000277165:Q4L	Q	+	2	0	FAM120A	95254029	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	4.854000	0.62918	0.149000	0.19098	0.358000	0.22013	CAG			0.821	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000053160.2		NM_014612	
COL15A1	1306	bcgsc.ca	37	9	101798650	101798650	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:101798650C>A	ENST00000375001.3	+	21	2804	c.2381C>A	c.(2380-2382)cCa>cAa	p.P794Q		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	794	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCGAGAGGGCCACCTGGGCAC	0.502																																					p.P794Q													.	COL15A1	211		0			c.C2381A												86.0	92.0	90.0					9																	101798650		2203	4300	6503	SO:0001583	missense	1306	exon21			GAGGGCCACCTGG	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2381C>A	9.37:g.101798650C>A	ENSP00000364140:p.Pro794Gln		103	0	0		55	0.07	4	NM_001855	67	0.00	0	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849348	0.32699	.	.	ENSG00000204291	ENST00000375001	D	0.90620	-2.7	5.39	2.55	0.30701	.	0.055575	0.64402	D	0.000001	D	0.92231	0.7536	M	0.80332	2.49	0.09310	N	0.999993	D	0.64830	0.994	P	0.58721	0.844	D	0.83425	0.0035	10	0.17832	T	0.49	-0.1616	7.7783	0.29049	0.0:0.7372:0.0:0.2628	.	794	P39059	COFA1_HUMAN	Q	794	ENSP00000364140:P794Q	ENSP00000364140:P794Q	P	+	2	0	COL15A1	100838471	0.218000	0.23608	0.067000	0.19924	0.969000	0.65631	1.623000	0.37008	0.347000	0.23924	-0.136000	0.14681	CCA			0.502	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000053386.3		NM_001855	
TTC16	158248	mdanderson.org	37	9	130487072	130487072	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:130487072G>T	ENST00000373289.3	+	9	1235	c.1155G>T	c.(1153-1155)gaG>gaT	p.E385D	PTRH1_ENST00000419060.1_5'UTR|TTC16_ENST00000489226.1_Intron|PTRH1_ENST00000429848.1_5'UTR|TTC16_ENST00000393748.4_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	385										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CCTTTGCCGAGGCGGACTACC	0.687																																					p.E385D													.	.			0			c.G1155T												14.0	14.0	14.0					9																	130487072		2194	4280	6474	SO:0001583	missense	158248	exon9			TGCCGAGGCGGAC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1155G>T	9.37:g.130487072G>T	ENSP00000362386:p.Glu385Asp		91	0	0		45	0.07	3	NM_144965	0		0	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592016	0.46214	.	.	ENSG00000167094	ENST00000373289	T	0.60171	0.21	4.86	2.82	0.32997	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.261284	0.27504	N	0.019061	T	0.53238	0.1784	L	0.46157	1.445	0.80722	D	1	P;P	0.43938	0.822;0.822	P;P	0.49528	0.614;0.614	T	0.56147	-0.8027	10	0.66056	D	0.02	-33.6883	4.4306	0.11525	0.089:0.151:0.6051:0.155	.	372;385	B4DZ42;Q8NEE8	.;TTC16_HUMAN	D	385	ENSP00000362386:E385D	ENSP00000362386:E385D	E	+	3	2	TTC16	129526893	1.000000	0.71417	1.000000	0.80357	0.114000	0.19823	0.972000	0.29409	2.250000	0.74265	0.313000	0.20887	GAG			0.687	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054224.1		NM_144965	
FPGS	2356	mdanderson.org	37	9	130572100	130572100	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:130572100G>T	ENST00000373247.2	+	12	1248	c.1198G>T	c.(1198-1200)Gag>Tag	p.E400*	FPGS_ENST00000373245.1_Silent_p.A350A|FPGS_ENST00000373225.3_Nonsense_Mutation_p.E350*|FPGS_ENST00000393706.2_Nonsense_Mutation_p.E374*|FPGS_ENST00000460181.1_3'UTR	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	400					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GCAGGGCCGCGAGAGGCCGAG	0.781																																					p.E400X													.	.			0			c.G1198T												2.0	3.0	3.0					9																	130572100		785	1873	2658	SO:0001587	stop_gained	2356	exon12			GGCCGCGAGAGGC		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.1198G>T	9.37:g.130572100G>T	ENSP00000362344:p.Glu400*		19	0	0		9	0.22	2	NM_004957	12	0.00	0	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Nonsense_Mutation	SNP	ENST00000373247.2	37	CCDS35148.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.463500	0.84425	.	.	ENSG00000136877	ENST00000373247;ENST00000393706;ENST00000373225	.	.	.	3.99	-0.659	0.11424	.	0.582613	0.18200	N	0.148544	.	.	.	.	.	.	0.23174	N	0.99817	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-11.1996	5.8095	0.18457	0.1993:0.3252:0.4755:0.0	.	.	.	.	X	400;374;350	.	ENSP00000362322:E350X	E	+	1	0	FPGS	129611921	0.008000	0.16893	0.000000	0.03702	0.018000	0.09664	0.262000	0.18460	-0.558000	0.06118	0.305000	0.20034	GAG			0.781	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054251.1			
SEC16A	9919	bcgsc.ca	37	9	139355646	139355646	+	Silent	SNP	G	G	A	rs375805476		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:139355646G>A	ENST00000371706.3	-	11	4473	c.4440C>T	c.(4438-4440)caC>caT	p.H1480H	SEC16A_ENST00000431893.2_Silent_p.H1480H|SEC16A_ENST00000290037.6_Silent_p.H1480H|SEC16A_ENST00000313050.7_Silent_p.H1658H			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1480					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TGACTCGGGCGTGTGTCCGGC	0.617																																					p.H1658H													.	SEC16A	249		0			c.C4974T							G		0,4236		0,0,2118	71.0	78.0	76.0		4974	-3.8	0.9	9		76	1,8459		0,1,4229	no	coding-synonymous	SEC16A	NM_014866.1		0,1,6347	AA,AG,GG		0.0118,0.0,0.0079		1658/2358	139355646	1,12695	2118	4230	6348	SO:0001819	synonymous_variant	9919	exon13			TCGGGCGTGTGTC	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.4440C>T	9.37:g.139355646G>A			99	0	0		59	0.07	4	NM_014866	57	0.00	0	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																						0.617	SEC16A-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000055077.1		XM_088459	
FAM157B	100132403	broad.mit.edu	37	9	141124391	141124392	+	lincRNA	DEL	TG	TG	-	rs367820400		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chr9:141124391_141124392delTG	ENST00000446912.2	+	0	906							P0CG42	F157B_HUMAN	family with sequence similarity 157, member B																		TAATGTGTTTTGTTTTTTTTTT	0.376																																					.													.	.			0			.																																											0	.			GTGTTTTGTTTTT			9q34	2013-01-24			ENSG00000233013	ENSG00000233013			34080	other	unknown							Standard	NM_001145249		Approved		uc011mfe.1	P0CG42	OTTHUMG00000021000		9.37:g.141124391_141124392delTG			47	0	0		91	0.14	13	.	0		0		RNA	DEL	ENST00000446912.2	37																																																																																						0.376	FAM157B-001	KNOWN	mRNA_end_NF|basic	lincRNA	lincRNA		OTTHUMT00000055378.2		NM_001145249	
G6PD	2539	mdanderson.org	37	X	153762708	153762708	+	Silent	SNP	G	G	T	rs80149725		TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chrX:153762708G>T	ENST00000393564.2	-	6	601	c.489C>A	c.(487-489)ggC>ggA	p.G163G	G6PD_ENST00000393562.2_Silent_p.G193G|G6PD_ENST00000497281.1_5'Flank|G6PD_ENST00000369620.2_Silent_p.G163G	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	163			G -> D (in Plymouth; class I). {ECO:0000269|PubMed:7858267}.|G -> S (in Mahidol; class III; reduced activity; associated with reduced density of Plasmodium vivax but not Plasmodium falciparum in Southeast Asians).		carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCGGTTCCAGCCTCTGCTGG	0.617																																					p.G193G													.	.			0			c.C579A												67.0	57.0	60.0					X																	153762708		2203	4300	6503	SO:0001819	synonymous_variant	2539	exon6			GTTCCAGCCTCTG	X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.489C>A	X.37:g.153762708G>T			41	0	0		30	0.10	3	NM_000402	207	0.00	1	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Silent	SNP	ENST00000393564.2	37	CCDS44023.1																																																																																					0.617	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000061170.3		NM_000402	
ZFY	7544	mdanderson.org	37	Y	2829680	2829680	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAGS-01A-11D-A42Y-10	TCGA-2G-AAGS-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	316c085e-6dd0-48c8-abc3-1653d58f11e4	f7149d2b-099b-4a37-a78b-54186de35097	g.chrY:2829680G>T	ENST00000155093.3	+	3	948	c.627G>T	c.(625-627)atG>atT	p.M209I	ZFY_ENST00000449237.1_Missense_Mutation_p.M183I|ZFY_ENST00000383052.1_Missense_Mutation_p.M209I|ZFY_ENST00000431102.1_Intron	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	209					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						ACTACCTAATGATTTCGTGTA	0.398																																					p.M209I													.	.			0			c.G627T												53.0	41.0	44.0					Y																	2829680		597	1957	2554	SO:0001583	missense	7544	exon3			CCTAATGATTTCG	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"""Zinc fingers, C2H2-type"""	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.627G>T	Y.37:g.2829680G>T	ENSP00000155093:p.Met209Ile		27	0.037037037	1		16	0.13	2	NM_003411	13	0.00	0	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Missense_Mutation	SNP	ENST00000155093.3	37	CCDS14774.1																																																																																					0.398	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000088063.1		NM_003411	
