#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CCDC126	90693	hgsc.bcm.edu	37	7	23682719	23682719	+	Silent	SNP	G	G	A	rs368070236		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr7:23682719G>A	ENST00000307471.3	+	4	865	c.408G>A	c.(406-408)tcG>tcA	p.S136S	CCDC126_ENST00000409765.1_Silent_p.S136S|CCDC126_ENST00000410069.1_Silent_p.S136S	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	136					protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)	p.S136S(1)		endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						CGAATGTCTCGGGCAGTATCA	0.428																																																	1	Substitution - coding silent(1)	ovary(1)	7						G		2,4404	4.2+/-10.8	0,2,2201	89.0	75.0	80.0		408	-9.3	0.6	7		80	0,8600		0,0,4300	no	coding-synonymous	CCDC126	NM_138771.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		136/141	23682719	2,13004	2203	4300	6503	23649244	SO:0001819	synonymous_variant	90693			BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193			22398	protein-coding gene	gene with protein product						12477932	Standard	NM_138771		Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.408G>A	7.37:g.23682719G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23649244	A8K1J6|Q6UWP1|Q75MQ6	Silent	SNP	ENST00000307471.3	37	CCDS5384.1																																																																																				CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250259.1	NM_138771	
PLCB1	23236	hgsc.bcm.edu	37	20	8755294	8755294	+	Missense_Mutation	SNP	G	G	T	rs139859188	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr20:8755294G>T	ENST00000338037.6	+	27	3066	c.3039G>T	c.(3037-3039)caG>caT	p.Q1013H	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Missense_Mutation_p.Q1013H|PLCB1_ENST00000378641.3_Missense_Mutation_p.Q1013H	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1013					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.Q1013H(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						ACAAACAACAGCAGCAGCTGC	0.418																																																	1	Substitution - Missense(1)	lung(1)	20											108.0	108.0	108.0					20																	8755294		2203	4300	6503	8703294	SO:0001583	missense	23236			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3039G>T	20.37:g.8755294G>T	ENSP00000338185:p.Gln1013His	Somatic		Capture	Illumina HiSeq	Phase_I	8703294	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.992039	0.54041	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.47528	0.84;0.84;0.84	5.63	3.29	0.37713	PLC-beta, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40546	0.1121	L	0.56769	1.78	0.58432	D	0.99999	P;B	0.36789	0.57;0.335	B;B	0.33960	0.173;0.134	T	0.15896	-1.0421	10	0.36615	T	0.2	.	10.27	0.43477	0.1883:0.0:0.8117:0.0	.	1013;1013	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	H	1013;1013;1013;933;933	ENSP00000367908:Q1013H;ENSP00000338185:Q1013H;ENSP00000367904:Q1013H	ENSP00000338185:Q1013H	Q	+	3	2	PLCB1	8703294	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.659000	0.37387	0.491000	0.27793	0.650000	0.86243	CAG		PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
ZBP1	81030	hgsc.bcm.edu	37	20	56190003	56190003	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr20:56190003T>C	ENST00000371173.3	-	4	619	c.442A>G	c.(442-444)Aag>Gag	p.K148E	ZBP1_ENST00000343535.4_Missense_Mutation_p.K148E|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000395822.3_Missense_Mutation_p.K73E|ZBP1_ENST00000541799.1_Missense_Mutation_p.K148E|ZBP1_ENST00000340462.4_Missense_Mutation_p.K125E	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	148					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TGCCTGCTCTTCATCCTGTAC	0.562																																																	0			20											246.0	196.0	213.0					20																	56190003		2203	4300	6503	55623409	SO:0001583	missense	81030			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.442A>G	20.37:g.56190003T>C	ENSP00000360215:p.Lys148Glu	Somatic		Capture	Illumina HiSeq	Phase_I	55623409	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.846520	0.32606	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	3.39	1.07	0.20283	Winged helix-turn-helix transcription repressor DNA-binding (1);Double-stranded RNA-specific adenosine deaminase (DRADA) (1);	1.361350	0.04816	N	0.436027	T	0.22666	0.0547	N	0.08118	0	0.09310	N	1	B;B;B;B	0.24651	0.046;0.108;0.108;0.108	B;B;B;B	0.22386	0.008;0.026;0.039;0.026	T	0.20706	-1.0267	10	0.44086	T	0.13	-6.4876	3.591	0.07989	0.0:0.1227:0.2294:0.6479	.	148;148;73;148	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	E	148;73;125;148;148;148	ENSP00000360215:K148E;ENSP00000379167:K73E;ENSP00000344954:K125E;ENSP00000340584:K148E;ENSP00000440552:K148E	ENSP00000344954:K125E	K	-	1	0	ZBP1	55623409	0.010000	0.17322	0.023000	0.16930	0.296000	0.27459	-0.232000	0.09055	0.200000	0.20447	0.533000	0.62120	AAG		ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
ARID4A	5926	hgsc.bcm.edu	37	14	58831429	58831429	+	Silent	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr14:58831429A>G	ENST00000355431.3	+	20	2995	c.2622A>G	c.(2620-2622)ggA>ggG	p.G874G	ARID4A_ENST00000348476.3_Silent_p.G874G|ARID4A_ENST00000395168.3_Silent_p.G874G|ARID4A_ENST00000431317.2_Silent_p.G874G	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	874					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G874G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TTGAGAATGGAATGGAAATGA	0.333																																																	1	Substitution - coding silent(1)	ovary(1)	14											69.0	64.0	66.0					14																	58831429		2203	4298	6501	57901182	SO:0001819	synonymous_variant	5926			S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2622A>G	14.37:g.58831429A>G		Somatic		Capture	Illumina HiSeq	Phase_I	57901182	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																				ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
CEP89	84902	hgsc.bcm.edu	37	19	33424370	33424370	+	Silent	SNP	C	C	T	rs138753622		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr19:33424370C>T	ENST00000305768.5	-	8	961	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CEP89_ENST00000590597.2_Silent_p.A291A	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	291					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.A291A(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CCTGTGACGACGCCTTCTCAG	0.383																																																	1	Substitution - coding silent(1)	ovary(1)	19						C		1,4405	2.1+/-5.4	0,1,2202	209.0	189.0	196.0		873	-10.2	0.0	19	dbSNP_134	196	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CEP89	NM_032816.3		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		291/784	33424370	6,13000	2203	4300	6503	38116210	SO:0001819	synonymous_variant	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.873G>A	19.37:g.33424370C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38116210	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																				CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
ST18	9705	hgsc.bcm.edu	37	8	53025885	53025885	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:53025885T>C	ENST00000276480.7	-	26	3700	c.3017A>G	c.(3016-3018)gAg>gGg	p.E1006G		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	1006					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E1006V(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				AAAATTCTGCTCACTGATAGG	0.433																																																	1	Substitution - Missense(1)	ovary(1)	8											125.0	109.0	115.0					8																	53025885		2203	4300	6503	53188438	SO:0001583	missense	9705			AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.3017A>G	8.37:g.53025885T>C	ENSP00000276480:p.Glu1006Gly	Somatic		Capture	Illumina HiSeq	Phase_I	53188438	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.029609	0.93518	.	.	ENSG00000147488	ENST00000276480	T	0.54675	0.56	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.71736	0.3375	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74500	-0.3645	10	0.87932	D	0	-25.6995	16.4416	0.83903	0.0:0.0:0.0:1.0	.	1006	O60284	ST18_HUMAN	G	1006	ENSP00000276480:E1006G	ENSP00000276480:E1006G	E	-	2	0	ST18	53188438	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.285000	0.76669	0.477000	0.44152	GAG		ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1		
PLEKHF2	79666	hgsc.bcm.edu	37	8	96166990	96166990	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:96166990G>T	ENST00000315367.3	+	2	959	c.718G>T	c.(718-720)Gat>Tat	p.D240Y	PLEKHF2_ENST00000519516.1_Missense_Mutation_p.D240Y	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	240					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)	p.D240N(1)		breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					TGATATGTCTGATGATGATGA	0.438																																																	1	Substitution - Missense(1)	ovary(1)	8											77.0	74.0	75.0					8																	96166990		2203	4300	6503	96236166	SO:0001583	missense	79666			AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"""Zinc fingers, FYVE domain containing"", ""Pleckstrin homology (PH) domain containing"""	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.718G>T	8.37:g.96166990G>T	ENSP00000322373:p.Asp240Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	96236166		Missense_Mutation	SNP	ENST00000315367.3	37	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619251	0.46736	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	D;D	0.81499	-1.5;-1.5	5.81	5.81	0.92471	.	0.090894	0.64402	D	0.000001	T	0.81098	0.4752	N	0.08118	0	0.80722	D	1	D	0.71674	0.998	D	0.67725	0.953	D	0.85140	0.0980	10	0.72032	D	0.01	-19.809	20.0925	0.97824	0.0:0.0:1.0:0.0	.	240	Q9H8W4	PKHF2_HUMAN	Y	240	ENSP00000322373:D240Y;ENSP00000427792:D240Y	ENSP00000322373:D240Y	D	+	1	0	PLEKHF2	96236166	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	9.080000	0.94040	2.756000	0.94617	0.557000	0.71058	GAT		PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613	
TRPS1	7227	hgsc.bcm.edu	37	8	116631434	116631434	+	Silent	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:116631434A>G	ENST00000220888.5	-	2	1011	c.852T>C	c.(850-852)cgT>cgC	p.R284R	TRPS1_ENST00000519674.1_Silent_p.R284R|TRPS1_ENST00000395715.3_Silent_p.R297R|TRPS1_ENST00000520276.1_Silent_p.R288R|TRPS1_ENST00000519076.1_Silent_p.R238R			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	284					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AAAACACAGAACGGTTGACCT	0.453									Langer-Giedion syndrome																																								0			8											96.0	90.0	92.0					8																	116631434		1919	4147	6066	116700609	SO:0001819	synonymous_variant	7227	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.852T>C	8.37:g.116631434A>G		Somatic		Capture	Illumina HiSeq	Phase_I	116700609	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
VAV3	10451	hgsc.bcm.edu	37	1	108313293	108313293	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:108313293C>T	ENST00000370056.4	-	6	887	c.613G>A	c.(613-615)Gaa>Aaa	p.E205K	VAV3_ENST00000371846.4_Missense_Mutation_p.E140K|VAV3_ENST00000527011.1_Missense_Mutation_p.E205K|VAV3_ENST00000343258.4_5'UTR	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	205	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.E205*(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		GTATATTTTTCTTCTGTCTGC	0.279																																																	1	Substitution - Nonsense(1)	ovary(1)	1											119.0	122.0	121.0					1																	108313293		2201	4298	6499	108114816	SO:0001583	missense	10451			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.613G>A	1.37:g.108313293C>T	ENSP00000359073:p.Glu205Lys	Somatic		Capture	Illumina HiSeq	Phase_I	108114816	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380261	0.82682	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.62105	0.05;0.05;0.05	5.8	5.8	0.92144	Dbl homology (DH) domain (5);Calponin homology domain (1);	0.052398	0.85682	D	0.000000	T	0.65386	0.2686	L	0.43152	1.355	0.58432	D	0.999999	B;D;B;D	0.64830	0.051;0.994;0.397;0.972	B;P;B;P	0.60682	0.041;0.842;0.304;0.878	T	0.59768	-0.7392	10	0.33940	T	0.23	.	20.0706	0.97721	0.0:1.0:0.0:0.0	.	205;205;140;205	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4	.;.;.;VAV3_HUMAN	K	205;205;140	ENSP00000359073:E205K;ENSP00000432540:E205K;ENSP00000360912:E140K	ENSP00000359073:E205K	E	-	1	0	VAV3	108114816	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.229000	0.78088	2.744000	0.94065	0.655000	0.94253	GAA		VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
INTS3	65123	hgsc.bcm.edu	37	1	153724879	153724879	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:153724879T>C	ENST00000318967.2	+	8	1422	c.854T>C	c.(853-855)tTc>tCc	p.F285S	RP11-216N14.9_ENST00000434575.1_RNA|INTS3_ENST00000456435.1_Missense_Mutation_p.F79S|snoU13_ENST00000458994.1_RNA|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000435409.2_Missense_Mutation_p.F285S|INTS3_ENST00000512605.1_Missense_Mutation_p.F79S|RP11-216N14.8_ENST00000453778.1_RNA	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	286					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGTCCTCAGTTCACAGGTAAG	0.448																																																	0			1											243.0	222.0	229.0					1																	153724879		2203	4300	6503	151991503	SO:0001583	missense	65123			BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.854T>C	1.37:g.153724879T>C	ENSP00000318641:p.Phe285Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151991503	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.255995	0.80246	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	3.99	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.74966	0.3786	M	0.86573	2.825	0.58432	D	0.999998	D;D;D	0.69078	0.981;0.997;0.997	D;D;D	0.79108	0.959;0.992;0.986	T	0.79964	-0.1581	9	0.87932	D	0	.	11.1537	0.48476	0.0:0.0:0.0:1.0	.	79;286;285	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	S	285;79;285;79	.	ENSP00000318641:F285S	F	+	2	0	INTS3	151991503	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.249000	0.78278	1.803000	0.52742	0.397000	0.26171	TTC		INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156926339	156926339	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:156926339G>A	ENST00000361409.2	-	18	2166	c.1424C>T	c.(1423-1425)gCc>gTc	p.A475V	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.A515V	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	475	RGSL. {ECO:0000255|PROSITE- ProRule:PRU00171}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|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(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGTATTGAGGGCGAAGTCCAT	0.532																																																	0			1											153.0	130.0	137.0					1																	156926339		2203	4300	6503	155192963	SO:0001583	missense	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.1424C>T	1.37:g.156926339G>A	ENSP00000354644:p.Ala475Val	Somatic		Capture	Illumina HiSeq	Phase_I	155192963	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477778	0.63849	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	D;D	0.83075	-1.68;-1.68	5.08	5.08	0.68730	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.53938	D	0.000060	T	0.81178	0.4768	L	0.35288	1.05	0.80722	D	1	D;D	0.89917	1.0;0.967	D;P	0.91635	0.999;0.742	T	0.76044	-0.3103	10	0.08837	T	0.75	-19.752	18.2585	0.90025	0.0:0.0:1.0:0.0	.	475;515	O15085;O15085-2	ARHGB_HUMAN;.	V	515;475	ENSP00000357177:A515V;ENSP00000354644:A475V	ENSP00000354644:A475V	A	-	2	0	ARHGEF11	155192963	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.446000	0.66600	2.635000	0.89317	0.585000	0.79938	GCC		ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
PYHIN1	149628	hgsc.bcm.edu	37	1	158914825	158914825	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:158914825T>C	ENST00000368140.1	+	7	1597	c.1352T>C	c.(1351-1353)tTc>tCc	p.F451S	PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Missense_Mutation_p.F442S|PYHIN1_ENST00000392252.3_Missense_Mutation_p.F442S|PYHIN1_ENST00000392254.2_Missense_Mutation_p.F451S	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	451					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AGCAGTTCCTTCACCAAGGTA	0.448																																																	0			1											136.0	137.0	136.0					1																	158914825		2203	4300	6503	157181449	SO:0001583	missense	149628			AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1352T>C	1.37:g.158914825T>C	ENSP00000357122:p.Phe451Ser	Somatic		Capture	Illumina HiSeq	Phase_I	157181449	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.527427	0.27299	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.04758	3.56;3.56;3.59;3.58	1.88	-2.46	0.06461	.	.	.	.	.	T	0.00875	0.0029	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.12630	0.006;0.006;0.006;0.003	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47649	-0.9101	9	0.87932	D	0	.	2.3064	0.04175	0.2301:0.4043:0.0:0.3655	.	442;451;442;451	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	S	451;442;451;442	ENSP00000357122:F451S;ENSP00000357120:F442S;ENSP00000376083:F451S;ENSP00000376082:F442S	ENSP00000357120:F442S	F	+	2	0	PYHIN1	157181449	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-1.181000	0.03085	-0.658000	0.05366	0.377000	0.23210	TTC		PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501	
USH2A	7399	hgsc.bcm.edu	37	1	216497642	216497642	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:216497642A>G	ENST00000307340.3	-	7	1582	c.1196T>C	c.(1195-1197)aTt>aCt	p.I399T	USH2A_ENST00000366943.2_Missense_Mutation_p.I399T|USH2A_ENST00000366942.3_Missense_Mutation_p.I399T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	399	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTCCTTTGAATCCTTATTTC	0.313										HNSCC(13;0.011)																																							0			1											85.0	91.0	89.0					1																	216497642		2200	4295	6495	214564265	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1196T>C	1.37:g.216497642A>G	ENSP00000305941:p.Ile399Thr	Somatic		Capture	Illumina HiSeq	Phase_I	214564265	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943170	0.73672	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;D;D	0.82619	-1.63;-1.63;-1.63	5.52	4.39	0.52855	Laminin, N-terminal (3);	0.305510	0.22328	N	0.061507	D	0.91102	0.7199	M	0.87269	2.87	0.58432	D	0.999999	D;P	0.89917	1.0;0.889	D;P	0.74348	0.983;0.526	D	0.91238	0.5019	10	0.87932	D	0	.	11.1893	0.48675	0.9279:0.0:0.0721:0.0	.	399;399	O75445-2;O75445	.;USH2A_HUMAN	T	399	ENSP00000305941:I399T;ENSP00000355910:I399T;ENSP00000355909:I399T	ENSP00000305941:I399T	I	-	2	0	USH2A	214564265	1.000000	0.71417	0.995000	0.50966	0.976000	0.68499	5.008000	0.63991	0.918000	0.36919	0.533000	0.62120	ATT		USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
OR8H2	390151	hgsc.bcm.edu	37	11	55872965	55872965	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr11:55872965T>C	ENST00000313503.1	+	1	447	c.447T>C	c.(445-447)taT>taC	p.Y149Y		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTGGGCCTTATGTGATTGGCT	0.458										HNSCC(53;0.14)																																							0			11											217.0	195.0	202.0					11																	55872965		2201	4296	6497	55629541	SO:0001819	synonymous_variant	390151			AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.447T>C	11.37:g.55872965T>C		Somatic		Capture	Illumina HiSeq	Phase_I	55629541	Q6IFC1	Silent	SNP	ENST00000313503.1	37	CCDS31518.1																																																																																				OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
PTGDR2	11251	hgsc.bcm.edu	37	11	60620803	60620803	+	Silent	SNP	C	C	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr11:60620803C>T	ENST00000332539.4	-	2	504	c.393G>A	c.(391-393)ctG>ctA	p.L131L	RP11-804A23.4_ENST00000538705.1_RNA	NM_004778.2	NP_004769.2	Q9Y5Y4	PD2R2_HUMAN	prostaglandin D2 receptor 2	131					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|calcium-mediated signaling (GO:0019722)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|prostaglandin D receptor activity (GO:0004956)|prostaglandin F receptor activity (GO:0004958)|prostaglandin J receptor activity (GO:0001785)	p.L131L(1)								Indomethacin(DB00328)|Sulindac(DB00605)	GCACCACCTGCAGGCAGCGGT	0.642																																																	1	Substitution - coding silent(1)	ovary(1)	11											18.0	19.0	19.0					11																	60620803		2198	4296	6494	60377379	SO:0001819	synonymous_variant	11251			AF118265	CCDS7994.1	11q12-q13.3	2012-08-08	2011-11-11	2011-11-11		ENSG00000183134		"""CD molecules"", ""GPCR / Class A : Prostanoid receptors"""	4502	protein-coding gene	gene with protein product	"""chemoattractant receptor homologous molecule expressed on T helper type 2 cells"""	604837	"""G protein-coupled receptor 44"""	GPR44		10036181	Standard	NM_004778		Approved	CRTH2, CD294, DP2	uc001nqc.2	Q9Y5Y4		ENST00000332539.4:c.393G>A	11.37:g.60620803C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60377379	O94765|Q4QRI6	Silent	SNP	ENST00000332539.4	37	CCDS7994.1																																																																																				PTGDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396328.1	NM_004778	
SUPT6H	6830	hgsc.bcm.edu	37	17	27030881	27030881	+	IGR	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr17:27030881A>G	ENST00000314616.6	+	0	6518				PROCA1_ENST00000439862.3_Silent_p.L238L|PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000301039.2_Silent_p.L236L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TTCTTAGTCAACTGGCCTTTC	0.483																																																	0			17											100.0	105.0	103.0					17																	27030881		2203	4300	6503	24055008	SO:0001628	intergenic_variant	147011			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27030881A>G		Somatic		Capture	Illumina HiSeq	Phase_I	24055008	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
LRRC37B	114659	hgsc.bcm.edu	37	17	30376234	30376234	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr17:30376234A>G	ENST00000341671.7	+	10	2502	c.2497A>G	c.(2497-2499)Aca>Gca	p.T833A	LRRC37B_ENST00000327564.7_Missense_Mutation_p.T860A|LRRC37B_ENST00000584368.1_Missense_Mutation_p.T794A|LRRC37B_ENST00000394713.3_Missense_Mutation_p.T782A|LRRC37B_ENST00000543378.2_Missense_Mutation_p.T751A	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	833						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				ATGTTCAGAAACACATGTGCA	0.488																																																	0			17											89.0	80.0	83.0					17																	30376234		2203	4300	6503	27400347	SO:0001583	missense	114659			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"""KIAA0563-related"""					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.2497A>G	17.37:g.30376234A>G	ENSP00000340519:p.Thr833Ala	Somatic		Capture	Illumina HiSeq	Phase_I	27400347	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	1.155	-0.645590	0.03531	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	1.78	-3.57	0.04612	.	.	.	.	.	T	0.30665	0.0772	M	0.76574	2.34	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49051	-0.8979	9	0.02654	T	1	.	4.0288	0.09700	0.2639:0.4144:0.3217:0.0	.	782;833	Q17RC9;Q96QE4	.;LR37B_HUMAN	A	751;860;782;833	ENSP00000443345:T751A;ENSP00000332536:T860A;ENSP00000378202:T782A;ENSP00000340519:T833A	ENSP00000332536:T860A	T	+	1	0	LRRC37B	27400347	0.000000	0.05858	0.008000	0.14137	0.000000	0.00434	-0.854000	0.04299	-1.484000	0.01856	-0.956000	0.02647	ACA		LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888	
KCNJ15	3772	hgsc.bcm.edu	37	21	39671269	39671269	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr21:39671269T>C	ENST00000328656.4	+	4	389	c.86T>C	c.(85-87)gTc>gCc	p.V29A	KCNJ15_ENST00000398938.2_Missense_Mutation_p.V29A|KCNJ15_ENST00000398932.1_Missense_Mutation_p.V29A|KCNJ15_ENST00000398934.1_Missense_Mutation_p.V29A|KCNJ15_ENST00000398930.1_Missense_Mutation_p.V29A	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	29					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	AGACCCCGCGTCATGTCCAAG	0.552																																																	0			21											98.0	79.0	86.0					21																	39671269		2203	4300	6503	38593139	SO:0001583	missense	3772			Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.86T>C	21.37:g.39671269T>C	ENSP00000331698:p.Val29Ala	Somatic		Capture	Illumina HiSeq	Phase_I	38593139	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.356052	0.82243	.	.	ENSG00000157551	ENST00000549805;ENST00000547341;ENST00000549932;ENST00000547595;ENST00000548700;ENST00000551422;ENST00000328656;ENST00000398928;ENST00000398925;ENST00000443341;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	T;T;T;T;T;T;D;D;T;T;D;D;D;D;D;D;D	0.94576	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-2.56;-3.09;-0.88;-0.42;-2.56;-2.56;-2.91;-2.56;-2.56;-3.09;-3.46	5.08	5.08	0.68730	.	0.138110	0.48767	U	0.000175	D	0.92335	0.7568	L	0.38175	1.15	0.58432	D	0.999998	P	0.51653	0.947	P	0.47075	0.536	D	0.91725	0.5392	10	0.35671	T	0.21	.	15.1426	0.72623	0.0:0.0:0.0:1.0	.	29	Q99712	IRK15_HUMAN	A	29	ENSP00000448770:V29A;ENSP00000447111:V29A;ENSP00000448676:V29A;ENSP00000450254:V29A;ENSP00000448886:V29A;ENSP00000449419:V29A;ENSP00000331698:V29A;ENSP00000381902:V29A;ENSP00000381899:V29A;ENSP00000413013:V29A;ENSP00000381911:V29A;ENSP00000381905:V29A;ENSP00000414487:V29A;ENSP00000381904:V29A;ENSP00000381907:V29A;ENSP00000381901:V29A;ENSP00000400849:V29A	ENSP00000331698:V29A	V	+	2	0	KCNJ15	38593139	1.000000	0.71417	0.995000	0.50966	0.924000	0.55760	7.803000	0.85983	2.047000	0.60756	0.383000	0.25322	GTC		KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
MKL2	57496	hgsc.bcm.edu	37	16	14339512	14339512	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr16:14339512T>C	ENST00000341243.5	+	9	1174	c.1174T>C	c.(1174-1176)Tta>Cta	p.L392L	MKL2_ENST00000574045.1_Silent_p.L403L|MKL2_ENST00000571589.1_Silent_p.L403L|MKL2_ENST00000318282.5_Silent_p.L403L			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	392	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.L403V(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCTGGATGACTTAAAGGTGAC	0.433																																																	1	Substitution - Missense(1)	ovary(1)	16											156.0	139.0	144.0					16																	14339512		2197	4300	6497	14247013	SO:0001819	synonymous_variant	57496			AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1174T>C	16.37:g.14339512T>C		Somatic		Capture	Illumina HiSeq	Phase_I	14247013	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	37																																																																																					MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048	
SMAD4	4089	hgsc.bcm.edu	37	18	48604721	48604721	+	Missense_Mutation	SNP	A	A	G	rs377767372|rs121912579		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr18:48604721A>G	ENST00000342988.3	+	12	2081	c.1543A>G	c.(1543-1545)Aga>Gga	p.R515G	SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.R419G|SMAD4_ENST00000398417.2_Missense_Mutation_p.R515G	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	515	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.	Necessary for heterotrimerization.			atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.R515*(3)|p.?(2)|p.R515fs*22(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGATTACCCAAGACAGAGCAT	0.498																																																	42	Whole gene deletion(36)|Substitution - Nonsense(3)|Unknown(2)|Deletion - Frameshift(1)	pancreas(30)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											104.0	98.0	100.0					18																	48604721		2203	4300	6503	46858719	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1543A>G	18.37:g.48604721A>G	ENSP00000341551:p.Arg515Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46858719	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.271137	0.59649	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.99688	-6.41;-6.41	6.08	4.93	0.64822	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.100580	0.64402	D	0.000002	D	0.99486	0.9817	H	0.95611	3.695	0.80722	D	1	P	0.34615	0.459	B	0.37346	0.247	D	0.97837	1.0266	10	0.87932	D	0	.	11.9417	0.52905	0.5591:0.4409:0.0:0.0	.	515	Q13485	SMAD4_HUMAN	G	515	ENSP00000341551:R515G;ENSP00000381452:R515G	ENSP00000341551:R515G	R	+	1	2	SMAD4	46858719	0.985000	0.35326	0.998000	0.56505	0.998000	0.95712	2.856000	0.48341	1.113000	0.41760	0.533000	0.62120	AGA		SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
ANKRD28	23243	hgsc.bcm.edu	37	3	15727739	15727739	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:15727739C>A	ENST00000399451.2	-	19	2318	c.1951G>T	c.(1951-1953)Gga>Tga	p.G651*	ANKRD28_ENST00000383777.1_Nonsense_Mutation_p.G684*|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	651						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGTCCATTTCCATCTTGAATA	0.368																																																	0			3											131.0	111.0	118.0					3																	15727739		1900	4117	6017	15702743	SO:0001587	stop_gained	23243			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1951G>T	3.37:g.15727739C>A	ENSP00000382379:p.Gly651*	Somatic		Capture	Illumina HiSeq	Phase_I	15702743	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Nonsense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	C	40	8.459582	0.98820	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	.	.	.	X	651;684;651	.	ENSP00000373287:G684X	G	-	1	0	ANKRD28	15702743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.718000	0.92993	0.655000	0.94253	GGA		ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199	
SLC22A13	9390	hgsc.bcm.edu	37	3	38307445	38307445	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:38307445T>C	ENST00000311856.4	+	1	143	c.94T>C	c.(94-96)Tct>Cct	p.S32P	SLC22A13_ENST00000450935.2_5'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	32					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		CAACTTCCTGTCTCCCTTCTA	0.502																																																	0			3											219.0	182.0	194.0					3																	38307445		2203	4300	6503	38282449	SO:0001583	missense	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"""Solute carriers"""	8494	protein-coding gene	gene with protein product		604047	"""organic cationic transporter-like 3"", ""solute carrier family 22 (organic anion transporter), member 13"""	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.94T>C	3.37:g.38307445T>C	ENSP00000310241:p.Ser32Pro	Somatic		Capture	Illumina HiSeq	Phase_I	38282449	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	37	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	.	4.528	0.097917	0.08681	.	.	ENSG00000172940	ENST00000311856	T	0.65549	-0.16	4.55	-9.11	0.00711	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.848720	0.02502	N	0.090608	T	0.69788	0.3150	M	0.78637	2.42	0.09310	N	0.999998	P;P	0.51147	0.942;0.836	P;P	0.52881	0.712;0.519	T	0.74090	-0.3777	10	0.34782	T	0.22	.	11.8312	0.52297	0.6963:0.0:0.2063:0.0974	.	32;32	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	P	32	ENSP00000310241:S32P	ENSP00000310241:S32P	S	+	1	0	SLC22A13	38282449	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.530000	0.00944	-3.802000	0.00105	-0.433000	0.05886	TCT		SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256	
CTNNB1	1499	hgsc.bcm.edu	37	3	41267276	41267276	+	Missense_Mutation	SNP	A	A	G	rs35288908	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:41267276A>G	ENST00000349496.5	+	6	1140	c.860A>G	c.(859-861)aAc>aGc	p.N287S	CTNNB1_ENST00000396183.3_Missense_Mutation_p.N287S|CTNNB1_ENST00000453024.1_Missense_Mutation_p.N280S|CTNNB1_ENST00000396185.3_Missense_Mutation_p.N287S|CTNNB1_ENST00000405570.1_Missense_Mutation_p.N287S	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	287					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.N287S(2)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GCCTTGCTCAACAAAACAAAT	0.388		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)			Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	2	Substitution - Missense(2)	large_intestine(2)	3	GRCh37	CM043757	CTNNB1	M	rs35288908	A	SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	122.0	119.0	120.0		860,860,860	5.7	1.0	3	dbSNP_126	120	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense,missense	CTNNB1	NM_001098209.1,NM_001098210.1,NM_001904.3	46,46,46	0,13,6490	GG,GA,AA		0.1395,0.0227,0.1	benign,benign,benign	287/782,287/782,287/782	41267276	13,12993	2203	4300	6503	41242280	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.860A>G	3.37:g.41267276A>G	ENSP00000344456:p.Asn287Ser	Somatic		Capture	Illumina HiSeq	Phase_I	41242280	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370081	0.24771	2.27E-4	0.001395	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.184600	0.56097	D	0.000034	T	0.37598	0.1009	N	0.02315	-0.6	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28933	-1.0028	10	0.20519	T	0.43	-1.1628	16.0129	0.80417	1.0:0.0:0.0:0.0	rs35288908	215;287	B4DSW9;P35222	.;CTNB1_HUMAN	S	287;287;287;280;287	ENSP00000385604:N287S;ENSP00000379486:N287S;ENSP00000344456:N287S;ENSP00000411226:N280S;ENSP00000379488:N287S	ENSP00000344456:N287S	N	+	2	0	CTNNB1	41242280	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.328000	0.65887	2.184000	0.69523	0.482000	0.46254	AAC		CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
BBX	56987	hgsc.bcm.edu	37	3	107497277	107497277	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:107497277C>A	ENST00000325805.8	+	13	2401	c.2114C>A	c.(2113-2115)cCt>cAt	p.P705H	BBX_ENST00000473542.1_3'UTR|BBX_ENST00000402543.1_Missense_Mutation_p.P705H|BBX_ENST00000406780.1_Missense_Mutation_p.P705H|BBX_ENST00000416476.2_Missense_Mutation_p.L369M|BBX_ENST00000415149.2_Missense_Mutation_p.P705H			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	705	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P705L(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CAATATAGTCCTGTTACATTT	0.418																																																	1	Substitution - Missense(1)	ovary(1)	3											96.0	96.0	96.0					3																	107497277		2203	4300	6503	108979967	SO:0001583	missense	56987			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2114C>A	3.37:g.107497277C>A	ENSP00000319974:p.Pro705His	Somatic		Capture	Illumina HiSeq	Phase_I	108979967	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.36|19.36	3.812354|3.812354	0.70912|0.70912	.|.	.|.	ENSG00000114439|ENSG00000114439	ENST00000416476|ENST00000415149;ENST00000402543;ENST00000325805;ENST00000406780	D|T;T;T;T	0.99136|0.61627	-5.47|0.09;0.09;0.09;0.09	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69860|0.69860	0.3158|0.3158	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D;D|D;D	0.89917|0.89917	1.0;0.996|1.0;1.0	D;P|D;D	0.78314|0.97110	0.991;0.823|1.0;0.998	T|T	0.71241|0.71241	-0.4651|-0.4651	9|10	0.87932|0.87932	D|D	0|0	-9.5728|-9.5728	20.327|20.327	0.98704|0.98704	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	16;369|705;705	Q9NRU5;A2RRM7|Q8WY36;Q8WY36-2	.;.|BBX_HUMAN;.	M|H	369|705	ENSP00000403860:L369M|ENSP00000408358:P705H;ENSP00000385317:P705H;ENSP00000319974:P705H;ENSP00000385530:P705H	ENSP00000403860:L369M|ENSP00000319974:P705H	L|P	+|+	1|2	2|0	BBX|BBX	108979967|108979967	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	7.487000|7.487000	0.81328|0.81328	2.794000|2.794000	0.96219|0.96219	0.650000|0.650000	0.86243|0.86243	CTG|CCT		BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
GPR149	344758	hgsc.bcm.edu	37	3	154055524	154055524	+	Silent	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:154055524A>G	ENST00000389740.2	-	4	2259	c.2160T>C	c.(2158-2160)gcT>gcC	p.A720A		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	720					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTTTCTGTAAGCTTTATTTA	0.433																																																	0			3											315.0	291.0	299.0					3																	154055524		1910	4118	6028	155538218	SO:0001819	synonymous_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2160T>C	3.37:g.154055524A>G		Somatic		Capture	Illumina HiSeq	Phase_I	155538218		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																				GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
ABCF3	55324	hgsc.bcm.edu	37	3	183909026	183909026	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:183909026G>T	ENST00000429586.2	+	16	1737	c.1552G>T	c.(1552-1554)Gag>Tag	p.E518*	EIF2B5_ENST00000444495.1_Intron|ABCF3_ENST00000292808.5_Nonsense_Mutation_p.E512*	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	518	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCTGATCTCGAGTCTCGCAT	0.537																																																	0			3											189.0	163.0	171.0					3																	183909026		2203	4300	6503	185391720	SO:0001587	stop_gained	55324			U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1552G>T	3.37:g.183909026G>T	ENSP00000411471:p.Glu518*	Somatic		Capture	Illumina HiSeq	Phase_I	185391720	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Nonsense_Mutation	SNP	ENST00000429586.2	37	CCDS3254.1	.	.	.	.	.	.	.	.	.	.	G	39	7.839535	0.98519	.	.	ENSG00000161204	ENST00000429586;ENST00000292808	.	.	.	5.93	5.93	0.95920	.	0.100946	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-25.7026	19.3249	0.94258	0.0:0.0:1.0:0.0	.	.	.	.	X	518;512	.	ENSP00000292808:E512X	E	+	1	0	ABCF3	185391720	1.000000	0.71417	0.977000	0.42913	0.993000	0.82548	9.476000	0.97823	2.805000	0.96524	0.655000	0.94253	GAG		ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358	
SLC12A6	9990	hgsc.bcm.edu	37	15	34529012	34529012	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr15:34529012T>C	ENST00000354181.3	-	23	3431	c.2939A>G	c.(2938-2940)gAc>gGc	p.D980G	SLC12A6_ENST00000558667.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000397702.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000558589.1_Missense_Mutation_p.D971G|SLC12A6_ENST00000458406.2_Missense_Mutation_p.D921G|SLC12A6_ENST00000560611.1_Missense_Mutation_p.D980G|SLC12A6_ENST00000451844.2_Missense_Mutation_p.D792G|SLC12A6_ENST00000290209.5_Missense_Mutation_p.D929G|SLC12A6_ENST00000397707.2_Missense_Mutation_p.D965G|SLC12A6_ENST00000560164.1_Missense_Mutation_p.D792G			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	980					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TATATCACTGTCATGCTGCCA	0.428																																																	0			15											126.0	110.0	115.0					15																	34529012		2201	4298	6499	32316304	SO:0001583	missense	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.2939A>G	15.37:g.34529012T>C	ENSP00000346112:p.Asp980Gly	Somatic		Capture	Illumina HiSeq	Phase_I	32316304	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654574	0.67472	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.16	5.16	0.70880	.	0.051702	0.64402	D	0.000001	T	0.58018	0.2093	M	0.84585	2.705	0.80722	D	1	P;P;P;B	0.41748	0.717;0.761;0.594;0.278	P;B;B;B	0.47864	0.559;0.354;0.356;0.15	T	0.66089	-0.6010	10	0.87932	D	0	.	14.1126	0.65132	0.0:0.0:0.0:1.0	.	965;980;929;792	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	G	929;965;971;921;921;792	ENSP00000290209:D929G;ENSP00000380819:D965G;ENSP00000380814:D921G;ENSP00000387725:D921G;ENSP00000390199:D792G	ENSP00000290209:D929G	D	-	2	0	SLC12A6	32316304	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.868000	0.87116	2.174000	0.68829	0.528000	0.53228	GAC		SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
TSPAN7	7102	hgsc.bcm.edu	37	X	38530641	38530641	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chrX:38530641T>C	ENST00000378482.2	+	3	459	c.282T>C	c.(280-282)ttT>ttC	p.F94F	TSPAN7_ENST00000422612.2_Silent_p.F120F|TSPAN7_ENST00000488893.1_3'UTR|TSPAN7_ENST00000286824.6_Silent_p.F111F|TSPAN7_ENST00000545599.1_Silent_p.F68F|TM4SF2_ENST00000465127.1_Silent_p.F124F	NM_004615.3	NP_004606.2	P41732	TSN7_HUMAN	tetraspanin 7	94					viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	11						ATGCCATGTTTCTGTCCCTGG	0.443																																																	0			X											371.0	314.0	333.0					X																	38530641		2202	4300	6502	38415585	SO:0001819	synonymous_variant	7102			D29808	CCDS14248.1	Xp11.4	2013-02-14	2005-03-21	2005-03-21	ENSG00000156298	ENSG00000156298		"""CD molecules"", ""Tetraspanins"""	11854	protein-coding gene	gene with protein product		300096	"""transmembrane 4 superfamily member 2"", ""mental retardation, X-linked 58"""	MXS1, TM4SF2, MRX58		12070254	Standard	NM_004615		Approved	DXS1692E, TALLA-1, A15, CD231	uc004deg.4	P41732	OTTHUMG00000024090	ENST00000378482.2:c.282T>C	X.37:g.38530641T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38415585	B2R5W7|D3DWB1|Q8WVG5|Q9UEY9	Silent	SNP	ENST00000378482.2	37	CCDS14248.1																																																																																				TSPAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356412.1		
FBXW7	55294	hgsc.bcm.edu	37	4	153251905	153251905	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr4:153251905T>C	ENST00000281708.4	-	7	2330	c.1101A>G	c.(1099-1101)cgA>cgG	p.R367R	FBXW7_ENST00000393956.3_Silent_p.R191R|FBXW7_ENST00000263981.5_Silent_p.R287R|FBXW7_ENST00000603841.1_Silent_p.R367R|FBXW7_ENST00000296555.5_Silent_p.R249R|FBXW7_ENST00000603548.1_Silent_p.R367R	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	367					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAGTTCTCCTCGCCTCCAGT	0.393			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4											331.0	284.0	300.0					4																	153251905		2203	4300	6503	153471355	SO:0001819	synonymous_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1101A>G	4.37:g.153251905T>C		Somatic		Capture	Illumina HiSeq	Phase_I	153471355	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	37	CCDS3777.1																																																																																				FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
NEIL3	55247	hgsc.bcm.edu	37	4	178283452	178283452	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr4:178283452T>C	ENST00000264596.3	+	10	1763	c.1645T>C	c.(1645-1647)Ttg>Ctg	p.L549L		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	549					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		GTGGGCAGATTTGTCCTTCCC	0.393								Base excision repair (BER), DNA glycosylases																																									0			4											85.0	86.0	86.0					4																	178283452		2203	4300	6503	178520446	SO:0001819	synonymous_variant	55247			AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1645T>C	4.37:g.178283452T>C		Somatic		Capture	Illumina HiSeq	Phase_I	178520446	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																				NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
EHBP1	23301	hgsc.bcm.edu	37	2	63101560	63101560	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:63101560A>G	ENST00000263991.5	+	11	1665	c.1183A>G	c.(1183-1185)Agg>Ggg	p.R395G	EHBP1_ENST00000405015.3_Missense_Mutation_p.R360G|EHBP1_ENST00000405289.1_Missense_Mutation_p.R360G|EHBP1_ENST00000431489.1_Missense_Mutation_p.R360G|EHBP1_ENST00000354487.3_Missense_Mutation_p.R360G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	395			R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGAAACTGAAAGGCGAGTGAA	0.378																																																	0			2											98.0	108.0	104.0					2																	63101560		2203	4300	6503	62955064	SO:0001583	missense	23301			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.1183A>G	2.37:g.63101560A>G	ENSP00000263991:p.Arg395Gly	Somatic		Capture	Illumina HiSeq	Phase_I	62955064	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242526	0.39598	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T	0.74002	-0.8;-0.8;-0.79;-0.79;-0.79	5.13	3.95	0.45737	.	0.467690	0.24752	N	0.035895	T	0.62073	0.2398	L	0.43152	1.355	0.37765	D	0.926455	P;B;B	0.35684	0.515;0.13;0.009	B;B;B	0.29862	0.108;0.022;0.031	T	0.59984	-0.7351	10	0.20046	T	0.44	.	12.0596	0.53555	0.8503:0.1497:0.0:0.0	.	360;360;395	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	G	360;360;395;360;360	ENSP00000384143:R360G;ENSP00000403783:R360G;ENSP00000263991:R395G;ENSP00000346482:R360G;ENSP00000385524:R360G	ENSP00000263991:R395G	R	+	1	2	EHBP1	62955064	1.000000	0.71417	0.992000	0.48379	0.964000	0.63967	3.296000	0.51802	0.884000	0.36064	0.528000	0.53228	AGG		EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
TMEM131	23505	hgsc.bcm.edu	37	2	98392471	98392471	+	Silent	SNP	T	T	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:98392471T>C	ENST00000186436.5	-	32	4383	c.4155A>G	c.(4153-4155)aaA>aaG	p.K1385K		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1385	Lys-rich.					integral component of membrane (GO:0016021)		p.K1272K(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						GCTGAAGAGGTTTTCCTTTCC	0.433																																																	1	Substitution - coding silent(1)	ovary(1)	2											155.0	150.0	151.0					2																	98392471		1879	4104	5983	97758903	SO:0001819	synonymous_variant	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.4155A>G	2.37:g.98392471T>C		Somatic		Capture	Illumina HiSeq	Phase_I	97758903		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																				TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
ZC3H6	376940	hgsc.bcm.edu	37	2	113067586	113067586	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr2:113067586A>G	ENST00000409871.1	+	4	862	c.461A>G	c.(460-462)gAc>gGc	p.D154G	ZC3H6_ENST00000343936.4_Missense_Mutation_p.D154G	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	154							metal ion binding (GO:0046872)	p.D154G(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TACAGTGATGACAACTTTGGT	0.363																																																	1	Substitution - Missense(1)	ovary(1)	2											77.0	72.0	74.0					2																	113067586		1881	4113	5994	112784057	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.461A>G	2.37:g.113067586A>G	ENSP00000386764:p.Asp154Gly	Somatic		Capture	Illumina HiSeq	Phase_I	112784057	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.618229	0.46736	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15718	2.4;2.4	3.09	3.09	0.35607	.	1.025170	0.07767	N	0.951061	T	0.12817	0.0311	N	0.22421	0.69	0.33846	D	0.632094	P	0.34522	0.455	B	0.34093	0.175	T	0.20806	-1.0264	10	0.66056	D	0.02	-16.8445	7.9401	0.29952	1.0:0.0:0.0:0.0	.	154	P61129	ZC3H6_HUMAN	G	154;154;131	ENSP00000386764:D154G;ENSP00000340298:D154G	ENSP00000340298:D154G	D	+	2	0	ZC3H6	112784057	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.476000	0.60216	1.671000	0.50874	0.459000	0.35465	GAC		ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
CTSL	1514	hgsc.bcm.edu	37	9	90343678	90343678	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr9:90343678A>G	ENST00000343150.5	+	5	1465	c.575A>G	c.(574-576)gAt>gGt	p.D192G	CTSL_ENST00000340342.6_Missense_Mutation_p.D192G|CTSL_ENST00000495822.1_3'UTR|CTSL_ENST00000342020.5_Missense_Mutation_p.D192G			P07711	CATL1_HUMAN	cathepsin L	192					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										TATGTTCAGGATAATGGAGGC	0.483																																																	0			9											103.0	93.0	96.0					9																	90343678		2203	4300	6503	89533498	SO:0001583	missense	1514			X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"""Cathepsins"""	2537	protein-coding gene	gene with protein product		116880	"""cathepsin L1"""	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.575A>G	9.37:g.90343678A>G	ENSP00000345344:p.Asp192Gly	Somatic		Capture	Illumina HiSeq	Phase_I	89533498	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	37	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951815	0.53186	.	.	ENSG00000135047	ENST00000343150;ENST00000340342;ENST00000342020	T;T;T	0.23147	1.92;1.92;1.92	4.51	3.37	0.38596	Peptidase C1A, papain C-terminal (2);	0.141383	0.64402	D	0.000008	T	0.34424	0.0897	M	0.78344	2.41	0.80722	D	1	B	0.18310	0.027	B	0.33690	0.168	T	0.21143	-1.0254	10	0.66056	D	0.02	.	9.8521	0.41064	0.9186:0.0:0.0814:0.0	.	192	P07711	CATL1_HUMAN	G	192	ENSP00000345344:D192G;ENSP00000365061:D192G;ENSP00000340470:D192G	ENSP00000365061:D192G	D	+	2	0	CTSL1	89533498	1.000000	0.71417	0.001000	0.08648	0.019000	0.09904	5.154000	0.64894	0.757000	0.33036	0.533000	0.62120	GAT		CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912	
OMD	4958	hgsc.bcm.edu	37	9	95179145	95179145	+	Silent	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr9:95179145A>G	ENST00000375550.4	-	2	971	c.696T>C	c.(694-696)ccT>ccC	p.P232P	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	232					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TAAGTGAAGAAGGCAAACCAG	0.343			T	USP6	aneurysmal bone cysts																																			Dom	yes		9	9q22.31	4958	osteomodulin		M	0			9											102.0	103.0	103.0					9																	95179145		2203	4300	6503	94218966	SO:0001819	synonymous_variant	4958			AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	8134	protein-coding gene	gene with protein product	"""osteoadherin proteoglycan"""						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.696T>C	9.37:g.95179145A>G		Somatic		Capture	Illumina HiSeq	Phase_I	94218966	Q5TBF4	Silent	SNP	ENST00000375550.4	37	CCDS6696.1																																																																																				OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014	
PABPC3	5042	hgsc.bcm.edu	37	13	25671196	25671196	+	Missense_Mutation	SNP	G	G	T	rs552336745		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr13:25671196G>T	ENST00000281589.3	+	1	897	c.860G>T	c.(859-861)aGg>aTg	p.R287M		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	287					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAGCAAGATAGGATCACCAGA	0.403																																																	0			13											185.0	178.0	181.0					13																	25671196		2203	4300	6503	24569196	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.860G>T	13.37:g.25671196G>T	ENSP00000281589:p.Arg287Met	Somatic		Capture	Illumina HiSeq	Phase_I	24569196	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.132654	0.37630	.	.	ENSG00000151846	ENST00000281589	T	0.32272	1.46	0.875	-0.0746	0.13730	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.45126	U	0.000389	T	0.42494	0.1205	M	0.87038	2.855	0.46298	D	0.998971	P	0.51240	0.943	P	0.51135	0.66	T	0.35500	-0.9786	10	0.72032	D	0.01	.	5.4221	0.16405	0.2335:0.0:0.7665:0.0	.	287	Q9H361	PABP3_HUMAN	M	287	ENSP00000281589:R287M	ENSP00000281589:R287M	R	+	2	0	PABPC3	24569196	1.000000	0.71417	0.985000	0.45067	0.699000	0.40488	4.902000	0.63266	-0.085000	0.12573	-0.657000	0.03884	AGG		PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
PTEN	5728	hgsc.bcm.edu	37	10	89720864	89720864	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr10:89720864C>T	ENST00000371953.3	+	8	2372	c.1015C>T	c.(1015-1017)Cca>Tca	p.P339S	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	339	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.P339S(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.S338fs*1(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		ATACTTTTCTCCAAATTTTAA	0.328		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	54	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(3)|Substitution - Missense(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|thyroid(1)|large_intestine(1)|soft_tissue(1)|endometrium(1)	10											50.0	53.0	52.0					10																	89720864		2203	4299	6502	89710844	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.1015C>T	10.37:g.89720864C>T	ENSP00000361021:p.Pro339Ser	Somatic		Capture	Illumina HiSeq	Phase_I	89710844	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520567	0.85495	.	.	ENSG00000171862	ENST00000371953	D	0.86030	-2.06	5.37	5.37	0.77165	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.90587	0.7049	M	0.64170	1.965	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	D	0.89724	0.3921	9	.	.	.	-4.5206	19.0916	0.93228	0.0:1.0:0.0:0.0	.	339	P60484	PTEN_HUMAN	S	339	ENSP00000361021:P339S	.	P	+	1	0	PTEN	89710844	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.405000	0.80007	2.516000	0.84829	0.591000	0.81541	CCA		PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CDH18	1016	hgsc.bcm.edu	37	5	19571820	19571820	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:19571820A>G	ENST00000507958.1	-	10	2111	c.1121T>C	c.(1120-1122)gTt>gCt	p.V374A	CDH18_ENST00000506372.1_Missense_Mutation_p.V374A|CDH18_ENST00000274170.4_Missense_Mutation_p.V374A|CDH18_ENST00000502796.1_Missense_Mutation_p.V374A|CDH18_ENST00000511273.1_Missense_Mutation_p.V374A|CDH18_ENST00000382275.1_Missense_Mutation_p.V374A			Q13634	CAD18_HUMAN	cadherin 18, type 2	374	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TACATCCCCAACAATGATCTT	0.418																																																	0			5											154.0	128.0	137.0					5																	19571820		2203	4300	6503	19607577	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1121T>C	5.37:g.19571820A>G	ENSP00000425093:p.Val374Ala	Somatic		Capture	Illumina HiSeq	Phase_I	19607577	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.693288	0.88735	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;0.1;-0.62	5.17	5.17	0.71159	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.88980	0.6585	H	0.97023	3.925	0.51012	D	0.999908	D;P	0.67145	0.996;0.844	D;P	0.76071	0.987;0.801	D	0.92441	0.5962	9	.	.	.	.	14.131	0.65253	1.0:0.0:0.0:0.0	.	374;374	B4DHG6;Q13634	.;CAD18_HUMAN	A	374;374;374;374;374;374;320;374	ENSP00000371710:V374A;ENSP00000425093:V374A;ENSP00000274170:V374A;ENSP00000424931:V374A;ENSP00000422138:V374A;ENSP00000427383:V320A;ENSP00000425854:V374A	.	V	-	2	0	CDH18	19607577	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.808000	0.91939	2.095000	0.63458	0.533000	0.62120	GTT		CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
APC	324	hgsc.bcm.edu	37	5	112174316	112174316	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112174316C>T	ENST00000457016.1	+	16	3405	c.3025C>T	c.(3025-3027)Cat>Tat	p.H1009Y	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.H1009Y|APC_ENST00000508376.2_Missense_Mutation_p.H1009Y			P25054	APC_HUMAN	adenomatous polyposis coli	1009	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.H1009Y(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCATAAAATACATAGTGCAAA	0.363		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	2	Substitution - Missense(1)|Unknown(1)	urinary_tract(1)|skin(1)	5											87.0	87.0	87.0					5																	112174316		2202	4300	6502	112202215	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3025C>T	5.37:g.112174316C>T	ENSP00000413133:p.His1009Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	112202215	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.057203	0.55325	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94457	-2.67;-3.43;-2.67;-2.67;-2.85	5.76	5.76	0.90799	.	0.047871	0.85682	D	0.000000	D	0.92525	0.7626	L	0.44542	1.39	0.54753	D	0.999989	P;P	0.49185	0.92;0.92	B;B	0.40636	0.335;0.335	D	0.93212	0.6601	10	0.72032	D	0.01	-15.4009	19.9596	0.97236	0.0:1.0:0.0:0.0	.	1011;1009	Q4LE70;P25054	.;APC_HUMAN	Y	1009;991;1009;1009;1009	ENSP00000413133:H1009Y;ENSP00000423224:H991Y;ENSP00000257430:H1009Y;ENSP00000427089:H1009Y;ENSP00000423828:H1009Y	ENSP00000257430:H1009Y	H	+	1	0	APC	112202215	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.294000	0.78760	2.726000	0.93360	0.655000	0.94253	CAT		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175155	112175155	+	Silent	SNP	A	A	G			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112175155A>G	ENST00000457016.1	+	16	4244	c.3864A>G	c.(3862-3864)ggA>ggG	p.G1288G	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.G1288G|APC_ENST00000508376.2_Silent_p.G1288G			P25054	APC_HUMAN	adenomatous polyposis coli	1288	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)|p.C1289fs*16(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATGAAATAGGATGTAATCAGA	0.368		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	5											57.0	59.0	58.0					5																	112175155		2202	4300	6502	112203054	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3864A>G	5.37:g.112175155A>G		Somatic		Capture	Illumina HiSeq	Phase_I	112203054	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175622	112175622	+	Missense_Mutation	SNP	A	A	C			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr5:112175622A>C	ENST00000457016.1	+	16	4711	c.4331A>C	c.(4330-4332)cAa>cCa	p.Q1444P	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1444P|APC_ENST00000508376.2_Missense_Mutation_p.Q1444P			P25054	APC_HUMAN	adenomatous polyposis coli	1444	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.P1424fs*19(1)|p.K1192fs*3(1)|p.P1441fs*28(1)|p.S1436fs*22(1)|p.P1441fs*27(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CCACCTCCTCAAACAGCTCAA	0.468		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											111.0	97.0	102.0					5																	112175622		2202	4300	6502	112203521	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4331A>C	5.37:g.112175622A>C	ENSP00000413133:p.Gln1444Pro	Somatic		Capture	Illumina HiSeq	Phase_I	112203521	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	9.291	1.050634	0.19827	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90004	-2.6;-2.6;-2.6	6.17	5.0	0.66597	.	0.103035	0.64402	D	0.000002	T	0.80824	0.4697	N	0.24115	0.695	0.49582	D	0.999807	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.73142	-0.4076	9	.	.	.	-11.4032	12.9375	0.58322	0.745:0.255:0.0:0.0	.	1446;1444	Q4LE70;P25054	.;APC_HUMAN	P	1444	ENSP00000413133:Q1444P;ENSP00000257430:Q1444P;ENSP00000427089:Q1444P	.	Q	+	2	0	APC	112203521	0.989000	0.36119	0.789000	0.31954	0.930000	0.56654	2.810000	0.47979	1.137000	0.42214	0.533000	0.62120	CAA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
FMN2	56776	hgsc.bcm.edu	37	1	240370914	240370946	+	In_Frame_Del	DEL	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	-	rs199628038|rs193049501|rs562038978|rs141094573|rs4997328|rs4997329|rs188083977|rs145628188|rs71170718|rs371697625	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	GCCCCCTCTACCCGGAGCGGGAATACCTCCTCC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr1:240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENST00000319653.9	+	5	3032_3064	c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	c.(2800-2835)ctgccccctctacccggagcgggaatacctcctccg>ctg	p.PPLPGAGIPPP935del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	935	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1082R(1)|p.P1081P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACTCCCTCTGCCCCCTCTACCCGGAGCGGGAATACCTCCTCCGCCCCCTCTA	0.678																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	1								1432,2834		223,986,924						0.9	0.0		dbSNP_114	42	2115,6135		277,1561,2287	no	coding	FMN2	NM_020066.4		500,2547,3211	A1A1,A1R,RR		25.6364,33.5677,28.3397				3547,8969				238437569	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2802_2834delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	1.37:g.240370914_240370946delGCCCCCTCTACCCGGAGCGGGAATACCTCCTCC	ENSP00000318884:p.Pro935_Pro945del	Somatic		Capture	Illumina HiSeq	Phase_I	238437537	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
MUC4	4585	hgsc.bcm.edu	37	3	195506550	195506597	+	In_Frame_Del	DEL	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG	-	rs532272297|rs370049807|rs71291866|rs200317787|rs199907090|rs201177106|rs570854088|rs189628384|rs540229983|rs78035451|rs368695884|rs371889626|rs201481290|rs112574652|rs199621200|rs572850344|rs200685331|rs566845926|rs200845871|rs530312336|rs377184618|rs201891747|rs368854101|rs564784853	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG	GGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:195506550_195506597delGGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG	ENST00000463781.3	-	2	12313_12360	c.11854_11901delCCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACGCCACC	c.(11854-11901)cctcttcctgtcaccgacacttcctcagtatccacaggtcacgccaccdel	p.PLPVTDTSSVSTGHAT3952del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.PLPVTDTSSVSTGHAT3952del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P3952S(8)|p.A3966T(2)|p.D3957N(2)|p.P3954L(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CAGGAAGAGAGGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTCA	0.601																																																	14	Substitution - Missense(14)	stomach(5)|kidney(5)|endometrium(2)|skin(2)	3							,,	129,2745		33,63,1341					,,		0.0			11	382,5000		84,214,2393	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	117,277,3734	A1A1,A1R,RR		7.0977,4.4885,6.1894	,,	,,		511,7745				196991376	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11854_11901delCCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACGCCACC	3.37:g.195506550_195506597delGGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGG	ENSP00000417498:p.Pro3952_Thr3967del	Somatic		Capture	Illumina HiSeq	Phase_I	196991329	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195509031	195509078	+	In_Frame_Del	DEL	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	-	rs540650529|rs78565605|rs559337249|rs75721951|rs35479616|rs35658525|rs201338210|rs371017154|rs75309583|rs77818558|rs71634715|rs185913520|rs35533324	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENST00000463781.3	-	2	9832_9879	c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	c.(9373-9420)gacacttcctcagcatccacaggtcaggccaccgctcttcctgtcaccdel	p.DTSSASTGQATALPVT3125del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.DTSSASTGQATALPVT3125del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGCTGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGGTGACAGGA	0.593																																																	0			3																																								196993857	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	3.37:g.195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENSP00000417498:p.Asp3125_Thr3140del	Somatic		Capture	Illumina HiSeq	Phase_I	196993810	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del	Somatic		Capture	Illumina HiSeq	Phase_I	196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RP1L1	94137	hgsc.bcm.edu	37	8	10467671	10467673	+	In_Frame_Del	DEL	CTC	CTC	-	rs200084961|rs374739066		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:10467671_10467673delCTC	ENST00000382483.3	-	4	4158_4160	c.3935_3937delGAG	c.(3934-3939)ggagaa>gaa	p.G1312del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1328	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		tgcagcccttctccttctgttcc	0.488																																																	0			8																																								10505083	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3935_3937delGAG	8.37:g.10467671_10467673delCTC	ENSP00000371923:p.Gly1312del	Somatic		Capture	Illumina HiSeq	Phase_I	10505081	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10467681	10467686	+	In_Frame_Del	DEL	TCCTTC	TCCTTC	-	rs386722181		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	TCCTTC	TCCTTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr8:10467681_10467686delTCCTTC	ENST00000382483.3	-	4	4145_4150	c.3922_3927delGAAGGA	c.(3922-3927)gaaggadel	p.EG1308del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctccttctgttccttcttTAGTTTCC	0.485																																																	0			8								43,79,3686		3,0,37,3,73,1788						-0.4	0.0			135	362,29,7561		4,0,354,0,29,3589	no	codingComplex	RP1L1	NM_178857.5		7,0,391,3,102,5377	A1A1,A1A2,A1R,A2A2,A2R,RR		4.917,3.2038,4.3622				405,108,11247				10505096	SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3922_3927delGAAGGA	8.37:g.10467681_10467686delTCCTTC	ENSP00000371923:p.Glu1308_Gly1309del	Somatic		Capture	Illumina HiSeq	Phase_I	10505091	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
LURAP1L	286343	hgsc.bcm.edu	37	9	12775861	12775862	+	In_Frame_Ins	INS	-	-	GGCGGCGGC	rs3833707|rs139315731		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr9:12775861_12775862insGGCGGCGGC	ENST00000319264.3	+	1	842_843	c.147_148insGGCGGCGGC	c.(148-150)ggc>GGCGGCGGCggc	p.50_50G>GGGG	RP11-3L8.3_ENST00000417638.1_RNA|LURAP1L_ENST00000489107.1_3'UTR	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	53	Gly-rich.							p.G49_G50insGGG(2)|p.G50_G52delGGG(1)									gcggtggtggtggcggcggcgg	0.688																																																	3	Insertion - In frame(2)|Deletion - In frame(1)	large_intestine(1)|prostate(1)|central_nervous_system(1)	9																																								12765862	SO:0001652	inframe_insertion	286343			AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.157_165dupGGCGGCGGC	9.37:g.12775862_12775870dupGGCGGCGGC	ENSP00000321026:p.GlyGlyGly53dup	Somatic		Capture	Illumina HiSeq	Phase_I	12765861	Q5VZX7|Q8N923|Q8NCG2	In_Frame_Ins	INS	ENST00000319264.3	37	CCDS6473.1																																																																																				LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs	Somatic		Capture	Illumina HiSeq	Phase_I	1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	DEL	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	-			TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chrUnknown:0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT								None (None upstream) : None (None downstream)																								0																																																	0			17																																								263631	SO:0001628	intergenic_variant	400566																															Unknown.37:g.0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT		Somatic		Capture	Illumina HiSeq	Phase_I	263602		Frame_Shift_Del	DEL		37																																																																																				0								
ZNF516	9658	hgsc.bcm.edu	37	18	74090958	74090958	+	Frame_Shift_Del	DEL	G	G	-	rs398079646|rs398033573|rs56087742		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr18:74090958delG	ENST00000443185.2	-	5	3428	c.3111delC	c.(3109-3111)cccfs	p.P1037fs	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1037					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGTGTAGGACGGGGGGGCGCC	0.652													GGGGGG|GGGGGGG|GGGGGG|insertion	5008	1.0	1.0	1.0	5008	,	,		13278	1.0		1.0	False		,,,				2504	1.0																0			18								3517,17		1755,7,5	7.0	7.0	7.0			-0.6	0.0	18	dbSNP_131	33	7701,27		3846,9,9	no	frameshift	ZNF516	NM_014643.3		5601,16,14	A1A1,A1R,RR		0.3494,0.481,0.3907			74090958	11218,44	1730	3829	5559	72219946	SO:0001589	frameshift_variant	9658			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3111delC	18.37:g.74090958delG	ENSP00000394757:p.Pro1037fs	Somatic		Capture	Illumina HiSeq	Phase_I	72219946		Frame_Shift_Del	DEL	ENST00000443185.2	37																																																																																					ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																																	0			22								2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				28215568	SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
VCX2	51480	hgsc.bcm.edu	37	X	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-	rs1058237|rs144469326	byFrequency	TCGA-AH-6547-01A-11D-1826-10	TCGA-AH-6547-11A-02D-1826-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	92091e93-d312-4314-adec-10b94abe5e2b	ad630103-e656-49c4-9361-c6634513a61b	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																	0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs	Somatic		Capture	Illumina HiSeq	Phase_I	8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
