#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
RET	5979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	43609023	43609023	+	Silent	SNP	A	A	G			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr10:43609023A>G	ENST00000355710.3	+	10	2011	c.1779A>G	c.(1777-1779)ggA>ggG	p.G593G	RET_ENST00000340058.5_Silent_p.G593G	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	593			G -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G592_G607del(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TTGTTGGGGGACACGAGCCTG	0.642		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	1	Deletion - In frame(1)	thyroid(1)											22.0	24.0	23.0					10																	43609023		2201	4299	6500	SO:0001819	synonymous_variant	5979	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1779A>G	10.37:g.43609023A>G			A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																				0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		8	21	8	21
ABTB2	25841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	34176285	34176285	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr11:34176285G>A	ENST00000435224.2	-	15	3153	c.2729C>T	c.(2728-2730)aCa>aTa	p.T910I	ABTB2_ENST00000298992.2_Missense_Mutation_p.T724I	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	910	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CATGGATTCTGTTCCTCCGTA	0.592																																																0													184.0	160.0	168.0					11																	34176285		2202	4298	6500	SO:0001583	missense	25841			AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.2729C>T	11.37:g.34176285G>A	ENSP00000410157:p.Thr910Ile		A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614014	0.66672	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.65916	-0.18;-0.18	4.79	4.79	0.61399	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.72835	0.3510	L	0.48174	1.505	0.80722	D	1	D	0.64830	0.994	D	0.66497	0.944	T	0.72301	-0.4334	10	0.40728	T	0.16	-19.7166	18.1968	0.89825	0.0:0.0:1.0:0.0	.	724	Q8N961	ABTB2_HUMAN	I	910;724	ENSP00000410157:T910I;ENSP00000298992:T724I	ENSP00000298992:T724I	T	-	2	0	ABTB2	34132861	1.000000	0.71417	0.083000	0.20561	0.614000	0.37383	8.009000	0.88606	2.365000	0.80145	0.462000	0.41574	ACA		0.592	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		108	139	108	139
CTTN	2017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	70261803	70261803	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr11:70261803A>G	ENST00000301843.8	+	7	643	c.437A>G	c.(436-438)gAg>gGg	p.E146G	CTTN_ENST00000376561.3_Missense_Mutation_p.E146G|CTTN_ENST00000346329.3_Missense_Mutation_p.E146G	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	146					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		GGGAAGACTGAGAAGCATGCC	0.532																																																0													156.0	169.0	165.0					11																	70261803		2200	4294	6494	SO:0001583	missense	2017			AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.437A>G	11.37:g.70261803A>G	ENSP00000301843:p.Glu146Gly		Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.1|26.1	4.702034|4.702034	0.88924|0.88924	.|.	.|.	ENSG00000085733|ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561|ENST00000415461	T;T;T|.	0.36878|.	1.32;1.28;1.23|.	5.28|5.28	4.15|4.15	0.48705|0.48705	.|.	0.105137|.	0.64402|.	D|.	0.000006|.	T|T	0.77778|0.77778	0.4181|0.4181	M|M	0.88775|0.88775	2.98|2.98	0.80722|0.80722	D|D	1|1	D;D;P|.	0.89917|.	1.0;0.999;0.947|.	D;D;P|.	0.91635|.	0.999;0.992;0.817|.	T|T	0.79694|0.79694	-0.1696|-0.1696	10|5	0.66056|.	D|.	0.02|.	-53.3361|-53.3361	11.2715|11.2715	0.49142|0.49142	0.9281:0.0:0.0719:0.0|0.9281:0.0:0.0719:0.0	.|.	146;146;146|.	Q96H99;Q14247;Q8N707|.	.;SRC8_HUMAN;.|.	G|G	146|128	ENSP00000317189:E146G;ENSP00000301843:E146G;ENSP00000365745:E146G|.	ENSP00000301843:E146G|.	E|R	+|+	2|1	0|2	CTTN|CTTN	69939451|69939451	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.911000|0.911000	0.54048|0.54048	8.364000|8.364000	0.90105|0.90105	0.962000|0.962000	0.38057|0.38057	0.533000|0.533000	0.62120|0.62120	GAG|AGA		0.532	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		212	362	212	362
CWF19L2	143884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	107299708	107299708	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr11:107299708G>T	ENST00000282251.5	-	8	1277	c.1250C>A	c.(1249-1251)aCa>aAa	p.T417K	CWF19L2_ENST00000433523.1_Missense_Mutation_p.T417K	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	417							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		ACTCCATGATGTTAATCTTTC	0.418																																																0													198.0	191.0	194.0					11																	107299708		2201	4298	6499	SO:0001583	missense	143884			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1250C>A	11.37:g.107299708G>T	ENSP00000282251:p.Thr417Lys		A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	G	3.156	-0.173245	0.06421	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.22336	1.96;1.96	5.54	3.63	0.41609	.	1.081050	0.06959	N	0.816000	T	0.12646	0.0307	N	0.16368	0.405	0.09310	N	1	B	0.22983	0.078	B	0.18263	0.021	T	0.24870	-1.0148	10	0.09843	T	0.71	-0.8194	8.9273	0.35648	0.1818:0.0:0.8182:0.0	.	417	Q2TBE0	C19L2_HUMAN	K	417	ENSP00000282251:T417K;ENSP00000387533:T417K	ENSP00000282251:T417K	T	-	2	0	CWF19L2	106804918	0.005000	0.15991	0.046000	0.18839	0.124000	0.20399	1.522000	0.35921	1.452000	0.47756	0.591000	0.81541	ACA		0.418	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		42	527	42	527
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	59271321	59271321	+	Silent	SNP	C	C	T	rs369890620		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr12:59271321C>T	ENST00000320743.3	-	15	2683	c.2397G>A	c.(2395-2397)tcG>tcA	p.S799S	LRIG3_ENST00000379141.4_Silent_p.S739S	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	799					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CATCGTCTAACGATGGGGCTG	0.562			T	ROS1	NSCLC																																		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0								C	,	0,4406		0,0,2203	168.0	106.0	127.0		2217,2397	-10.9	0.0	12		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LRIG3	NM_001136051.1,NM_153377.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	739/1060,799/1120	59271321	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	121227			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2397G>A	12.37:g.59271321C>T			Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																				0.562	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		52	81	52	81
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	24826581	24826581	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr16:24826581C>T	ENST00000395799.3	+	19	4915	c.4786C>T	c.(4786-4788)Cgt>Tgt	p.R1596C	TNRC6A_ENST00000432286.2_Missense_Mutation_p.R74C|CTD-2515A14.1_ENST00000568895.1_RNA|TNRC6A_ENST00000315183.7_Missense_Mutation_p.R1547C	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1596					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TGGCTGGCCACGTGCCAAATC	0.448																																																0													86.0	81.0	83.0					16																	24826581		2197	4300	6497	SO:0001583	missense	27327			U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4786C>T	16.37:g.24826581C>T	ENSP00000379144:p.Arg1596Cys		C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.532363|4.532363	0.85812|0.85812	.|.	.|.	ENSG00000090905|ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286|ENST00000450465	T;T|.	0.14640|.	2.52;2.49|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72771|0.72771	0.3502|0.3502	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;0.978;0.993;1.0|.	P;P;P;D|.	0.64506|.	0.855;0.676;0.707;0.926|.	T|T	0.70659|0.70659	-0.4811|-0.4811	10|5	0.56958|.	D|.	0.05|.	-8.203|-8.203	15.0829|15.0829	0.72127|0.72127	0.1417:0.8583:0.0:0.0|0.1417:0.8583:0.0:0.0	.|.	263;735;1547;1596|.	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7|.	.;.;.;TNR6A_HUMAN|.	C|M	1547;1596;74|486	ENSP00000326900:R1547C;ENSP00000379144:R1596C|.	ENSP00000326900:R1547C|.	R|T	+|+	1|2	0|0	TNRC6A|TNRC6A	24734082|24734082	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.867000|4.867000	0.63013|0.63013	2.809000|2.809000	0.96659|0.96659	0.655000|0.655000	0.94253|0.94253	CGT|ACG		0.448	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		71	112	71	112
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578442	7578442	+	Missense_Mutation	SNP	T	T	C	rs148924904		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr17:7578442T>C	ENST00000269305.4	-	5	677	c.488A>G	c.(487-489)tAc>tGc	p.Y163C	TP53_ENST00000420246.2_Missense_Mutation_p.Y163C|TP53_ENST00000445888.2_Missense_Mutation_p.Y163C|TP53_ENST00000455263.2_Missense_Mutation_p.Y163C|TP53_ENST00000359597.4_Missense_Mutation_p.Y163C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.Y163C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	163	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y163C(134)|p.Y70C(12)|p.Y31C(12)|p.0?(8)|p.Y163S(7)|p.V157_C176del20(1)|p.Y31S(1)|p.Y163fs*1(1)|p.Y70S(1)|p.Y163_Q165delYKQ(1)|p.P151_V173del23(1)|p.Y163fs*14(1)|p.S149fs*72(1)|p.A159_Q167delAMAIYKQSQ(1)|p.I162_Y163delIY(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGACTGCTTGTAGATGGCCAT	0.622		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	183	Substitution - Missense(167)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)	lung(49)|breast(34)|haematopoietic_and_lymphoid_tissue(14)|ovary(14)|urinary_tract(13)|large_intestine(10)|upper_aerodigestive_tract(9)|central_nervous_system(7)|oesophagus(7)|stomach(6)|biliary_tract(6)|bone(4)|pancreas(3)|soft_tissue(2)|liver(2)|endometrium(1)|salivary_gland(1)|prostate(1)	GRCh37	CM942135	TP53	M	rs148924904						53.0	54.0	53.0					17																	7578442		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.488A>G	17.37:g.7578442T>C	ENSP00000269305:p.Tyr163Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.567047	0.45694	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99872	-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36	5.59	3.32	0.38043	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.062225	0.64402	D	0.000003	D	0.99746	0.9899	M	0.70595	2.14	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.996;0.999;0.983;0.999;1.0;0.999;0.994	D	0.98089	1.0408	10	0.87932	D	0	-16.6607	9.5833	0.39501	0.2797:0.0:0.0:0.7203	.	124;163;163;70;163;163;163	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	163;163;163;163;163;163;152;70;31;70;31;163	ENSP00000410739:Y163C;ENSP00000352610:Y163C;ENSP00000269305:Y163C;ENSP00000398846:Y163C;ENSP00000391127:Y163C;ENSP00000391478:Y163C;ENSP00000425104:Y31C;ENSP00000423862:Y70C;ENSP00000424104:Y163C	ENSP00000269305:Y163C	Y	-	2	0	TP53	7519167	1.000000	0.71417	0.998000	0.56505	0.050000	0.14768	5.141000	0.64814	0.446000	0.26666	0.533000	0.62120	TAC		0.622	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		139	20	139	20
NEK8	284086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	27065006	27065006	+	Silent	SNP	C	C	T			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr17:27065006C>T	ENST00000268766.6	+	7	1093	c.1059C>T	c.(1057-1059)ctC>ctT	p.L353L	AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	353					organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					CTGGGCGTCTCATCCTGTGGG	0.701																																					NSCLC(6;19 293 14866 25253 49845)											0													23.0	27.0	26.0					17																	27065006		2200	4297	6497	SO:0001819	synonymous_variant	284086			AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"""NIMA (never in mitosis gene a)- related kinase 8"""			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.1059C>T	17.37:g.27065006C>T			A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Silent	SNP	ENST00000268766.6	37	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.277432	0.23307	.	.	ENSG00000160602	ENST00000543014	T	0.70516	-0.49	5.58	1.41	0.22369	.	.	.	.	.	T	0.70544	0.3236	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66324	-0.5952	6	0.66056	D	0.02	.	4.8044	0.13312	0.1376:0.5685:0.0:0.2938	.	.	.	.	Y	407	ENSP00000465859:H407Y	ENSP00000446066:H407Y	H	+	1	0	NEK8	24089133	0.995000	0.38212	0.998000	0.56505	0.980000	0.70556	0.422000	0.21296	0.063000	0.16370	-0.136000	0.14681	CAT		0.701	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			45	57	45	57
SESN2	83667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	28598956	28598956	+	Silent	SNP	C	C	T	rs373209094		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr1:28598956C>T	ENST00000253063.3	+	4	837	c.516C>T	c.(514-516)ctC>ctT	p.L172L		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	172					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCATGGCTCATCACCAAGG	0.652																																																0								C		1,4405	2.1+/-5.4	0,1,2202	56.0	57.0	56.0		516	-3.4	1.0	1		56	0,8600		0,0,4300	no	coding-synonymous	SESN2	NM_031459.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		172/481	28598956	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	83667			AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.516C>T	1.37:g.28598956C>T			Q5T7D0|Q96SI5	Silent	SNP	ENST00000253063.3	37	CCDS321.1																																																																																				0.652	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1			63	100	63	100
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	152192510	152192510	+	Missense_Mutation	SNP	C	C	T	rs537328568	byFrequency	TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr1:152192510C>T	ENST00000368801.2	-	3	1670	c.1595G>A	c.(1594-1596)cGa>cAa	p.R532Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	532					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCCATGTCGGCTGTGTCC	0.567													C|||	3	0.000599042	0.0023	0.0	5008	,	,		22195	0.0		0.0	False		,,,				2504	0.0															0													181.0	184.0	183.0					1																	152192510		2203	4300	6503	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1595G>A	1.37:g.152192510C>T	ENSP00000357791:p.Arg532Gln		Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	5.220	0.226074	0.09916	.	.	ENSG00000197915	ENST00000368801	T	0.01705	4.68	2.47	-4.93	0.03066	.	.	.	.	.	T	0.00271	0.0008	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43245	-0.9403	9	0.12103	T	0.63	.	5.3679	0.16123	0.0:0.346:0.2653:0.3888	.	532	Q86YZ3	HORN_HUMAN	Q	532	ENSP00000357791:R532Q	ENSP00000357791:R532Q	R	-	2	0	HRNR	150459134	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.740000	0.04861	-2.308000	0.00652	-0.779000	0.03376	CGA		0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		45	414	45	414
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			54	118	54	118
DAW1	164781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	228750104	228750104	+	Missense_Mutation	SNP	G	G	C			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr2:228750104G>C	ENST00000309931.2	+	2	161	c.78G>C	c.(76-78)aaG>aaC	p.K26N	DAW1_ENST00000373666.2_Missense_Mutation_p.K26N|SNORA25_ENST00000607153.1_RNA|DAW1_ENST00000545118.1_Missense_Mutation_p.K11N	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	26						cilium (GO:0005929)											GAGAATTAAAGACTAAGTCCA	0.343																																																0													111.0	117.0	115.0					2																	228750104		2203	4300	6503	SO:0001583	missense	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"""WD repeat domain containing"""	26383	protein-coding gene	gene with protein product	"""outer row dynein assembly 16 homolog (Chlamydomonas)"""		"""WD repeat domain 69"""	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.78G>C	2.37:g.228750104G>C	ENSP00000311899:p.Lys26Asn		Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.014024	0.54468	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	T;T;T;T	0.55052	0.63;0.56;0.71;0.54	5.52	5.52	0.82312	.	0.105334	0.64402	D	0.000006	T	0.53465	0.1798	L	0.56769	1.78	0.50632	D	0.999883	P	0.47253	0.892	P	0.46299	0.511	T	0.57717	-0.7763	10	0.62326	D	0.03	.	10.3802	0.44108	0.0885:0.0:0.9115:0.0	.	26	Q8N136	WDR69_HUMAN	N	26;26;11;11	ENSP00000362770:K26N;ENSP00000311899:K26N;ENSP00000394853:K11N;ENSP00000437887:K11N	ENSP00000311899:K26N	K	+	3	2	WDR69	228458348	1.000000	0.71417	0.998000	0.56505	0.391000	0.30476	3.703000	0.54808	2.577000	0.86979	0.655000	0.94253	AAG		0.343	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		19	258	19	258
OR5H6	79295	hgsc.bcm.edu;broad.mit.edu	37	3	97983515	97983515	+	Silent	SNP	T	T	C			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr3:97983515T>C	ENST00000383696.2	+	1	428	c.387T>C	c.(385-387)ttT>ttC	p.F129F	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CAGAATGTTTTCTCTTGGCAA	0.368																																																0													100.0	87.0	92.0					3																	97983515		2202	4298	6500	SO:0001819	synonymous_variant	79295			BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.387T>C	3.37:g.97983515T>C			Q6IF88	Silent	SNP	ENST00000383696.2	37	CCDS33800.1																																																																																				0.368	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			26	290	26	290
PDE6B	5158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	659049	659049	+	Silent	SNP	A	A	G			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr4:659049A>G	ENST00000496514.1	+	19	2220	c.2199A>G	c.(2197-2199)gcA>gcG	p.A733A	PDE6B_ENST00000255622.6_Silent_p.A733A|PDE6B_ENST00000429163.2_Silent_p.A454A			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	733					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	TCCAGGTCGCACTTCTCGTGG	0.627																																					GBM(71;463 1194 9848 25922 46834)											0													60.0	56.0	57.0					4																	659049		2203	4299	6502	SO:0001819	synonymous_variant	5158			BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2199A>G	4.37:g.659049A>G			B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	5.971	0.363097	0.11296	.	.	ENSG00000133256	ENST00000461490	.	.	.	4.69	-3.29	0.05017	.	.	.	.	.	T	0.36552	0.0971	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36286	-0.9754	4	.	.	.	.	0.6123	0.00763	0.382:0.169:0.1215:0.3274	.	.	.	.	R	14	.	.	H	+	2	0	PDE6B	649049	0.032000	0.19561	0.898000	0.35279	0.425000	0.31504	-1.151000	0.03175	-0.320000	0.08640	-0.672000	0.03802	CAC		0.627	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		21	56	21	56
FOXP4	116113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	41554783	41554783	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr6:41554783C>T	ENST00000307972.4	+	5	559	c.547C>T	c.(547-549)Ctc>Ttc	p.L183F	FOXP4_ENST00000409208.1_Missense_Mutation_p.L183F|FOXP4_ENST00000373063.3_Missense_Mutation_p.L183F|FOXP4_ENST00000373057.3_Missense_Mutation_p.L181F|FOXP4_ENST00000373060.1_Missense_Mutation_p.L183F			Q8IVH2	FOXP4_HUMAN	forkhead box P4	183	Gln-rich.				embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCAGCAGCAGCTCCTGCAAAT	0.662											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																				0													24.0	27.0	26.0					6																	41554783		2198	4298	6496	SO:0001583	missense	116113			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.547C>T	6.37:g.41554783C>T	ENSP00000309823:p.Leu183Phe	902	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.388365	0.61956	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;D;T;T;T	0.92149	1.18;-2.98;1.18;1.18;1.18	4.57	4.57	0.56435	.	0.162851	0.41712	D	0.000825	D	0.93161	0.7822	M	0.80746	2.51	0.48087	D	0.999589	D;D;D	0.58970	0.984;0.984;0.984	P;P;P	0.55161	0.77;0.77;0.77	D	0.93348	0.6716	10	0.52906	T	0.07	.	12.8325	0.57754	0.0:0.9172:0.0:0.0828	.	183;181;183	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	F	183;183;183;181;183	ENSP00000362151:L183F;ENSP00000362154:L183F;ENSP00000386958:L183F;ENSP00000362148:L181F;ENSP00000309823:L183F	ENSP00000309823:L183F	L	+	1	0	FOXP4	41662761	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.656000	0.61483	2.073000	0.62155	0.561000	0.74099	CTC		0.662	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		9	71	9	71
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	129475728	129475728	+	Missense_Mutation	SNP	G	G	A	rs367649718		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr6:129475728G>A	ENST00000421865.2	+	8	1155	c.1106G>A	c.(1105-1107)cGt>cAt	p.R369H		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	369	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R369L(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTGAATATACGTGGAAAGTAC	0.388													g|||	1	0.000199681	0.0	0.0	5008	,	,		15017	0.0		0.0	False		,,,				2504	0.001															1	Substitution - Missense(1)	ovary(1)						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	92.0	92.0	92.0		1106,1106	2.4	1.0	6		92	0,8600		0,0,4300	no	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	369/3123,369/3119	129475728	1,13005	2203	4300	6503	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.1106G>A	6.37:g.129475728G>A	ENSP00000400365:p.Arg369His		Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	g	5.272	0.235698	0.10023	2.27E-4	0.0	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.33438	1.41	6.06	2.37	0.29283	EGF-like, laminin (3);	0.479957	0.22257	N	0.062465	T	0.01870	0.0059	N	0.01505	-0.83	0.23923	N	0.996455	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45190	-0.9278	10	0.05620	T	0.96	.	4.3752	0.11267	0.5978:0.0:0.1975:0.2046	.	369;369	A6NF00;P24043	.;LAMA2_HUMAN	H	369	ENSP00000400365:R369H	ENSP00000346769:R369H	R	+	2	0	LAMA2	129517421	0.951000	0.32395	0.994000	0.49952	0.934000	0.57294	1.741000	0.38238	0.166000	0.19597	-0.285000	0.09966	CGT		0.388	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			83	111	83	111
MACC1	346389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	20198861	20198861	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr7:20198861A>G	ENST00000400331.5	-	5	1431	c.1123T>C	c.(1123-1125)Tat>Cat	p.Y375H	MACC1_ENST00000332878.4_Missense_Mutation_p.Y375H|MACC1_ENST00000589011.1_Missense_Mutation_p.Y375H	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	375					positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						TTGGGTCCATAAATTCCAATT	0.398																																																0													55.0	51.0	52.0					7																	20198861		2203	4300	6503	SO:0001583	missense	346389				CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.1123T>C	7.37:g.20198861A>G	ENSP00000383185:p.Tyr375His		A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700109	0.68501	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.23348	1.91;1.91	5.72	5.72	0.89469	.	0.110120	0.64402	D	0.000004	T	0.52224	0.1721	M	0.78637	2.42	0.58432	D	0.999997	D	0.76494	0.999	D	0.67231	0.95	T	0.57376	-0.7822	10	0.87932	D	0	-11.2754	15.9957	0.80237	1.0:0.0:0.0:0.0	.	375	Q6ZN28	MACC1_HUMAN	H	375	ENSP00000383185:Y375H;ENSP00000328410:Y375H	ENSP00000328410:Y375H	Y	-	1	0	MACC1	20165386	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.339000	0.96797	2.172000	0.68678	0.482000	0.46254	TAT		0.398	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		66	95	66	95
SH2D3C	10044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	130507277	130507277	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr9:130507277C>T	ENST00000314830.8	-	7	1479	c.1366G>A	c.(1366-1368)Gcc>Acc	p.A456T	SH2D3C_ENST00000429553.1_Missense_Mutation_p.A102T|SH2D3C_ENST00000471939.1_5'UTR|SH2D3C_ENST00000373274.3_Missense_Mutation_p.A296T|SH2D3C_ENST00000373277.4_Missense_Mutation_p.A299T|SH2D3C_ENST00000420366.1_Missense_Mutation_p.A298T|SH2D3C_ENST00000373276.3_Missense_Mutation_p.A388T	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	456					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTCTTTGGGGCACTTCCGGGA	0.662																																																0													37.0	46.0	42.0					9																	130507277		2203	4298	6501	SO:0001583	missense	10044			AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.1366G>A	9.37:g.130507277C>T	ENSP00000317817:p.Ala456Thr		A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	37	CCDS6877.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586674	0.28268	.	.	ENSG00000095370	ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830	T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98	5.37	0.296	0.15757	.	1.010990	0.07890	N	0.971087	T	0.17152	0.0412	N	0.02011	-0.69	0.22745	N	0.998784	B;B;B;B;B	0.10296	0.0;0.0;0.003;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.001;0.002;0.001;0.002	T	0.25779	-1.0122	10	0.22706	T	0.39	-2.5162	8.5096	0.33208	0.0:0.4148:0.0:0.5852	.	296;456;388;299;298	E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.;SH2D3_HUMAN;.;.;.	T	299;298;388;296;102;456	ENSP00000362374:A299T;ENSP00000388536:A298T;ENSP00000362373:A388T;ENSP00000362371:A296T;ENSP00000394632:A102T;ENSP00000317817:A456T	ENSP00000317817:A456T	A	-	1	0	SH2D3C	129547098	0.000000	0.05858	0.996000	0.52242	0.779000	0.44077	-0.353000	0.07691	0.004000	0.14682	0.462000	0.41574	GCC		0.662	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		24	189	24	189
MAP7D3	79649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	135323365	135323365	+	Missense_Mutation	SNP	T	T	A			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chrX:135323365T>A	ENST00000316077.9	-	5	709	c.489A>T	c.(487-489)agA>agT	p.R163S	MAP7D3_ENST00000370661.1_Missense_Mutation_p.R163S|MAP7D3_ENST00000370663.5_Missense_Mutation_p.R145S	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	163					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CCCATGACCATCTTTTTTGCT	0.323																																																0													63.0	58.0	59.0					X																	135323365		1848	4104	5952	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.489A>T	X.37:g.135323365T>A	ENSP00000318086:p.Arg163Ser		A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.683890	0.47991	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.12361	2.69;2.69;2.69;2.69	5.15	-2.58	0.06228	.	.	.	.	.	T	0.31451	0.0797	M	0.69823	2.125	0.33080	D	0.53654	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.38222	-0.9671	9	0.72032	D	0.01	-35.4195	11.0289	0.47761	0.0:0.5115:0.0:0.4885	.	145;163;163;163	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	S	163;163;145;163	ENSP00000359695:R163S;ENSP00000318086:R163S;ENSP00000359697:R145S;ENSP00000359694:R163S	ENSP00000318086:R163S	R	-	3	2	MAP7D3	135151031	0.979000	0.34478	0.402000	0.26371	0.180000	0.23129	-0.147000	0.10234	-0.703000	0.05049	-0.453000	0.05500	AGA		0.323	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			91	137	91	137
IER3	8870	broad.mit.edu;ucsc.edu	37	6	30708275	30708275	+	IGR	SNP	G	G	A	rs139987312		TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr6:30708275G>A	ENST00000259874.5	-	0	1244				FLOT1_ENST00000456573.2_Missense_Mutation_p.R142W|FLOT1_ENST00000376389.3_Missense_Mutation_p.R190W|FLOT1_ENST00000470643.1_5'UTR|XXbac-BPG252P9.10_ENST00000607333.1_RNA	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						TCTCTCACCCGGATCCCAGCA	0.532													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20972	0.0		0.0	False		,,,				2504	0.0															0								G	TRP/ARG	5,3017		0,5,1506	100.0	90.0	93.0		568	2.8	1.0	6	dbSNP_134	93	0,5416		0,0,2708	yes	missense	FLOT1	NM_005803.2	101	0,5,4214	AA,AG,GG		0.0,0.1655,0.0593	probably-damaging	190/428	30708275	5,8433	1511	2708	4219	SO:0001628	intergenic_variant	10211			AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		6.37:g.30708275G>A			Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	37	CCDS4689.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	16.60	3.167768	0.57476	0.001655	0.0	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000413165;ENST00000438162;ENST00000418160;ENST00000445853;ENST00000416018	T;T;T;D;D	0.97752	1.25;1.23;1.25;-3.96;-4.52	4.66	2.81	0.32909	.	0.131690	0.49305	D	0.000149	D	0.96645	0.8905	M	0.83483	2.645	0.49389	D	0.999781	D;D	0.64830	0.994;0.994	P;P	0.51701	0.677;0.556	D	0.95819	0.8848	10	0.87932	D	0	-0.6315	5.7642	0.18217	0.0925:0.0:0.5667:0.3407	.	142;190	B4DVY7;O75955	.;FLOT1_HUMAN	W	190;142;127;190;95;190;174	ENSP00000365569:R190W;ENSP00000394375:R142W;ENSP00000400615:R190W;ENSP00000398834:R190W;ENSP00000412058:R174W	ENSP00000365569:R190W	R	-	1	2	FLOT1	30816254	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.595000	0.36708	1.166000	0.42689	-0.169000	0.13324	CGG		0.532	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2			106	143	106	143
WNT9B	7484	broad.mit.edu;ucsc.edu	37	17	44953783	44953783	+	Missense_Mutation	SNP	G	G	A	rs149931425	byFrequency	TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr17:44953783G>A	ENST00000290015.2	+	4	826	c.773G>A	c.(772-774)cGc>cAc	p.R258H	WNT9B_ENST00000393461.2_Missense_Mutation_p.R258H	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	258					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GCCTTGGGCCGCCTAGAGCTG	0.642													G|||	5	0.000998403	0.0	0.0	5008	,	,		20005	0.005		0.0	False		,,,				2504	0.0															0													50.0	48.0	49.0					17																	44953783		2203	4300	6503	SO:0001583	missense	7484			AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.773G>A	17.37:g.44953783G>A	ENSP00000290015:p.Arg258His		Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	13.32	2.203207	0.38905	.	.	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.76186	-1.0;-1.0	4.56	3.59	0.41128	.	0.133642	0.34828	N	0.003648	T	0.46560	0.1399	N	0.13098	0.295	0.37722	D	0.924964	B;B	0.18863	0.004;0.031	B;B	0.17722	0.008;0.019	T	0.51896	-0.8647	10	0.45353	T	0.12	.	7.471	0.27349	0.2468:0.0:0.7532:0.0	.	258;258	E7EPC3;O14905	.;WNT9B_HUMAN	H	252;258;258	ENSP00000377105:R258H;ENSP00000290015:R258H	ENSP00000290015:R258H	R	+	2	0	WNT9B	42308782	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.808000	0.55598	1.153000	0.42468	0.561000	0.74099	CGC		0.642	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		54	89	54	89
LIMCH1	22998	broad.mit.edu;ucsc.edu	37	4	41646515	41646515	+	Splice_Site	SNP	A	A	C			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr4:41646515A>C	ENST00000313860.7	+	10	1025		c.e10-1		LIMCH1_ENST00000512946.1_Splice_Site|LIMCH1_ENST00000509277.1_Splice_Site|LIMCH1_ENST00000381753.4_Splice_Site|LIMCH1_ENST00000513024.1_Splice_Site|LIMCH1_ENST00000503057.1_Splice_Site|LIMCH1_ENST00000512632.1_Splice_Site|LIMCH1_ENST00000512820.1_Splice_Site|LIMCH1_ENST00000514096.1_Splice_Site|LIMCH1_ENST00000508501.1_Splice_Site|LIMCH1_ENST00000511496.1_Splice_Site|LIMCH1_ENST00000396595.3_Splice_Site	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1						actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						CTCCACACTCAGGAGCACCAG	0.672											OREG0016169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													15.0	16.0	15.0					4																	41646515		2184	4270	6454	SO:0001630	splice_region_variant	22998			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.972-1A>C	4.37:g.41646515A>C		902	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Splice_Site	SNP	ENST00000313860.7	37	CCDS33977.1	.	.	.	.	.	.	.	.	.	.	A	16.25	3.068948	0.55539	.	.	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000508466	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5306	0.75956	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LIMCH1	41341272	1.000000	0.71417	0.998000	0.56505	0.278000	0.26855	8.372000	0.90127	2.135000	0.66039	0.460000	0.39030	.		0.672	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	Intron	10	9	10	9
C3P1	388503	broad.mit.edu;ucsc.edu	37	19	10165979	10165979	+	RNA	SNP	G	G	A			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr19:10165979G>A	ENST00000495140.1	+	0	1607							Q6ZMU1	C3P1_HUMAN	complement component 3 precursor pseudogene							extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)			endometrium(4)|large_intestine(2)|lung(6)|urinary_tract(1)	13						CACCTCCAAGGGGAACCCAGG	0.592																																																0													80.0	87.0	85.0					19																	10165979		2111	4228	6339			388503			AK131489		19p13.2	2009-04-08			ENSG00000167798	ENSG00000167798			34414	pseudogene	pseudogene							Standard	NR_027300		Approved	CPLP	uc010dwx.2	Q6ZMU1	OTTHUMG00000158555		19.37:g.10165979G>A				RNA	SNP	ENST00000495140.1	37																																																																																					0.592	C3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000351284.1	NR_027300		16	116	16	116
OR2T1	26696	broad.mit.edu;hgsc.bcm.edu	37	1	248570073	248570073	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr1:248570073delC	ENST00000366474.1	+	1	778	c.778delC	c.(778-780)cctfs	p.P260fs		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTGCTGATTCCTTTCTCTGT	0.507																																																0													282.0	236.0	251.0					1																	248570073		2203	4300	6503	SO:0001589	frameshift_variant	26696			U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.778delC	1.37:g.248570073delC	ENSP00000355430:p.Pro260fs		Q6IEZ9	Frame_Shift_Del	DEL	ENST00000366474.1	37	CCDS31115.1																																																																																				0.507	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			36	164	36	164
FAM208B	54906	broad.mit.edu;hgsc.bcm.edu	37	10	5784139	5784140	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chr10:5784139_5784140delAA	ENST00000328090.5	+	14	3032_3033	c.2407_2408delAA	c.(2407-2409)aatfs	p.N803fs	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	803																	GTTTTACAGCAATCAGAACAAA	0.396																																																0																																										SO:0001589	frameshift_variant	54906			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.2407_2408delAA	10.37:g.5784139_5784140delAA	ENSP00000328426:p.Asn803fs		Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Frame_Shift_Del	DEL	ENST00000328090.5	37	CCDS41485.1																																																																																				0.396	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		70	217	70	217
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76944356	76944356	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E1-5322-01A-01D-1468-08	TCGA-E1-5322-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52b650cf-fb99-462b-81a2-ce202f5c2eca	9b8501d7-1ba6-42ee-975c-dd1830d5a3a6	g.chrX:76944356delT	ENST00000373344.5	-	7	763	c.549delA	c.(547-549)aaafs	p.K183fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.K145fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	183	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.		Missing (in ATRX). {ECO:0000269|PubMed:10204841}.		ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AAATGGAATCTTTTTGAAAAT	0.353			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											155.0	144.0	147.0					X																	76944356		2203	4296	6499	SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.549delA	X.37:g.76944356delT	ENSP00000362441:p.Lys183fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		157	231	157	231
