#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABTB2	25841	hgsc.bcm.edu	37	11	34174107	34174107	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:34174107G>T	ENST00000435224.2	-	17	3329	c.2905C>A	c.(2905-2907)Ctg>Atg	p.L969M	ABTB2_ENST00000298992.2_Missense_Mutation_p.L783M	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	969					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)				TCACAGAACAGGGCCAGTTCT	0.592																																																	0													51.0	48.0	49.0					11																	34174107		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.2905C>A	11.37:g.34174107G>T	ENSP00000410157:p.Leu969Met	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809359	0.31961	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.59364	0.27;0.27	4.71	4.71	0.59529	.	0.541426	0.18356	N	0.143712	T	0.41743	0.1172	L	0.36672	1.1	0.29040	N	0.885132	P	0.36837	0.571	B	0.30495	0.116	T	0.47459	-0.9116	10	0.54805	T	0.06	.	7.1158	0.25416	0.1313:0.1624:0.7063:0.0	.	783	Q8N961	ABTB2_HUMAN	M	969;783	ENSP00000410157:L969M;ENSP00000298992:L783M	ENSP00000298992:L783M	L	-	1	2	ABTB2	34130683	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.730000	0.38125	2.156000	0.67533	0.462000	0.41574	CTG		0.592	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3		NM_145804	
ACAD10	80724	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	112193484	112193484	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr12:112193484G>A	ENST00000313698.4	+	20	3129	c.2974G>A	c.(2974-2976)Gat>Aat	p.D992N	ACAD10_ENST00000455480.2_Missense_Mutation_p.D1023N|RP11-162P23.2_ENST00000546840.2_Nonsense_Mutation_p.W13*	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	992						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.D992N(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						TGCAGCCTTGGATATAGCCAT	0.552																																																	1	Substitution - Missense(1)	kidney(1)											120.0	121.0	120.0					12																	112193484		2203	4300	6503	SO:0001583	missense	80724			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"""acyl-Coenzyme A dehydrogenase family, member 10"""			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2974G>A	12.37:g.112193484G>A	ENSP00000325137:p.Asp992Asn	Somatic		WXS	Illumina HiSeq	Phase_I	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.934946	0.52866	.	.	ENSG00000111271	ENST00000455480;ENST00000313698;ENST00000512792;ENST00000546899	D;D	0.96073	-3.9;-3.9	4.98	4.06	0.47325	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.421246	0.24539	N	0.037650	D	0.95544	0.8552	M	0.71920	2.185	0.80722	D	1	P;B	0.34997	0.479;0.188	B;B	0.43155	0.247;0.41	D	0.95403	0.8491	10	0.72032	D	0.01	.	14.1514	0.65387	0.0:0.1517:0.8483:0.0	.	1023;992	G3XAJ0;Q6JQN1	.;ACD10_HUMAN	N	1023;992;147;12	ENSP00000389813:D1023N;ENSP00000325137:D992N	ENSP00000325137:D992N	D	+	1	0	ACAD10	110677867	1.000000	0.71417	0.026000	0.17262	0.969000	0.65631	4.756000	0.62205	1.271000	0.44313	0.561000	0.74099	GAT		0.552	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1		NM_025247	
ACSL5	51703	hgsc.bcm.edu;ucsc.edu	37	10	114164332	114164332	+	Splice_Site	SNP	A	A	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr10:114164332A>T	ENST00000393081.1	+	4	636	c.329A>T	c.(328-330)cAg>cTg	p.Q110L	RP11-324O2.3_ENST00000449782.2_RNA|ACSL5_ENST00000356116.1_Splice_Site_p.Q166L|ACSL5_ENST00000354655.4_Splice_Site_p.Q110L|ACSL5_ENST00000433418.1_Splice_Site_p.Q110L|ACSL5_ENST00000354273.4_Splice_Site_p.Q110L|ACSL5_ENST00000479936.1_3'UTR|RP11-324O2.3_ENST00000594870.2_RNA|RP11-324O2.3_ENST00000598447.1_RNA	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	110					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		TCTTACAAACAGGTAAGTTGA	0.368																																																	0													83.0	84.0	83.0					10																	114164332		2203	4300	6503	SO:0001630	splice_region_variant	51703			AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.330+1A>T	10.37:g.114164332A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722533	0.89298	.	.	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	5.3	5.3	0.74995	AMP-dependent synthetase/ligase (1);	0.056394	0.64402	N	0.000001	T	0.74015	0.3661	H	0.95004	3.61	0.80722	D	1	D;P;P	0.56035	0.974;0.947;0.923	P;P;P	0.59424	0.857;0.726;0.756	T	0.82352	-0.0500	10	0.87932	D	0	-9.2697	14.5126	0.67797	1.0:0.0:0.0:0.0	.	110;166;110	A6GV77;Q9ULC5-3;Q9ULC5	.;.;ACSL5_HUMAN	L	110;110;166;110;110	ENSP00000346680:Q110L;ENSP00000376796:Q110L;ENSP00000348429:Q166L;ENSP00000403647:Q110L;ENSP00000346223:Q110L	ENSP00000346223:Q110L	Q	+	2	0	ACSL5	114154322	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	8.803000	0.91915	2.129000	0.65627	0.533000	0.62120	CAG		0.368	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1		NM_016234	Missense_Mutation
ADAMTS12	81792	broad.mit.edu;ucsc.edu	37	5	33683970	33683970	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr5:33683970C>T	ENST00000504830.1	-	4	1160	c.825G>A	c.(823-825)atG>atA	p.M275I	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.M275I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	275	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.M275I(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ATACCATGTTCATGATGGTGA	0.468										HNSCC(64;0.19)																																							1	Substitution - Missense(1)	kidney(1)											113.0	104.0	107.0					5																	33683970		2203	4300	6503	SO:0001583	missense	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.825G>A	5.37:g.33683970C>T	ENSP00000422554:p.Met275Ile	Somatic		WXS	Illumina GAIIx	Phase_I	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936581	0.73442	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59772	0.24;0.24	5.21	5.21	0.72293	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	M	0.70903	2.155	0.80722	D	1	B;D	0.63880	0.347;0.993	B;D	0.71870	0.12;0.975	T	0.74962	-0.3485	10	0.72032	D	0.01	.	13.5991	0.62010	0.0:0.9257:0.0:0.0743	.	275;275	P58397-3;P58397	.;ATS12_HUMAN	I	275	ENSP00000422554:M275I;ENSP00000344847:M275I	ENSP00000344847:M275I	M	-	3	0	ADAMTS12	33719727	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	3.751000	0.55165	2.870000	0.98441	0.637000	0.83480	ATG		0.468	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2		NM_030955	
AFTPH	54812	hgsc.bcm.edu;ucsc.edu	37	2	64808374	64808374	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:64808374delG	ENST00000422803.1	+	8	2820	c.2506delG	c.(2506-2508)gacfs	p.D836fs	AFTPH_ENST00000409933.1_Frame_Shift_Del_p.D836fs|RNU6-100P_ENST00000516605.1_RNA|AFTPH_ENST00000487769.1_Intron|AFTPH_ENST00000238856.4_Intron|AFTPH_ENST00000238855.7_Frame_Shift_Del_p.D836fs|AFTPH_ENST00000409183.1_Frame_Shift_Del_p.D467fs			Q6ULP2	AFTIN_HUMAN	aftiphilin	836					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GCCCGTGGATGACAGTAGCTC	0.463																																																	0													83.0	84.0	83.0					2																	64808374		1952	4157	6109	SO:0001589	frameshift_variant	54812			AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2506delG	2.37:g.64808374delG	ENSP00000397726:p.Asp836fs	Somatic		WXS	Illumina HiSeq	Phase_I	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Frame_Shift_Del	DEL	ENST00000422803.1	37																																																																																					0.463	AFTPH-202	KNOWN	basic	protein_coding	protein_coding			NM_017657	
AGL	178	broad.mit.edu;ucsc.edu	37	1	100368332	100368332	+	Missense_Mutation	SNP	C	C	G	rs113994131		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr1:100368332C>G	ENST00000294724.4	+	27	4160	c.3682C>G	c.(3682-3684)Cga>Gga	p.R1228G	AGL_ENST00000361915.3_Missense_Mutation_p.R1228G|AGL_ENST00000361302.3_Missense_Mutation_p.R1212G|AGL_ENST00000370163.3_Missense_Mutation_p.R1228G|AGL_ENST00000361522.4_Missense_Mutation_p.R1211G|AGL_ENST00000370165.3_Missense_Mutation_p.R1228G|AGL_ENST00000370161.2_Missense_Mutation_p.R1212G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1228					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)	p.R1228G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		CCAGATAGATCGAAACATGAA	0.373																																																	1	Substitution - Missense(1)	kidney(1)	GRCh37	CM960018	AGL	M	rs113994131						96.0	89.0	92.0					1																	100368332		2203	4300	6503	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3682C>G	1.37:g.100368332C>G	ENSP00000294724:p.Arg1228Gly	Somatic		WXS	Illumina GAIIx	Phase_I	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	C	8.270	0.813191	0.16537	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	6.14	4.1	0.47936	Six-hairpin glycosidase-like (1);	0.238346	0.39341	N	0.001397	T	0.58963	0.2159	L	0.55743	1.74	0.28388	N	0.919239	B;B;B	0.30634	0.288;0.288;0.181	B;B;B	0.36766	0.222;0.222;0.232	T	0.55952	-0.8059	10	0.27785	T	0.31	-22.643	15.7829	0.78275	0.3373:0.6627:0.0:0.0	.	1211;1212;1228	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	1228;1228;1228;1228;1212;1212;1211	ENSP00000355106:R1228G;ENSP00000359184:R1228G;ENSP00000359182:R1228G;ENSP00000294724:R1228G;ENSP00000354971:R1212G;ENSP00000359180:R1212G;ENSP00000354635:R1211G	ENSP00000294724:R1228G	R	+	1	2	AGL	100140920	0.990000	0.36364	0.980000	0.43619	0.232000	0.25224	2.363000	0.44178	1.598000	0.50083	0.637000	0.83480	CGA		0.373	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1		NM_000028	
ARPC2	10109	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	219093573	219093573	+	Splice_Site	SNP	G	G	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:219093573G>T	ENST00000295685.10	+	3	483	c.222G>T	c.(220-222)gaG>gaT	p.E74D	ARPC2_ENST00000315717.5_Splice_Site_p.E74D	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	74					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)	p.E74D(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		GTGCTGATGAGGTAAGATCCA	0.408																																																	1	Substitution - Missense(1)	kidney(1)											88.0	83.0	85.0					2																	219093573		2203	4300	6503	SO:0001630	splice_region_variant	10109			AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"""Actin related protein 2/3 complex subunits"""	705	protein-coding gene	gene with protein product		604224	"""actin related protein 2/3 complex, subunit 2 (34 kD)"""			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.222+1G>T	2.37:g.219093573G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	37	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.603717	0.66445	.	.	ENSG00000163466	ENST00000315717;ENST00000420104;ENST00000295685	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.56470	0.1987	L	0.41356	1.27	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.46748	-0.9169	9	0.27785	T	0.31	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	74	O15144	ARPC2_HUMAN	D	74	.	ENSP00000295685:E74D	E	+	3	2	ARPC2	218801818	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.620000	0.98373	2.941000	0.99782	0.655000	0.94253	GAG		0.408	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2		NM_005731	Missense_Mutation
AQP12B	653437	broad.mit.edu	37	2	241622318	241622318	+	5'Flank	SNP	C	C	T	rs201727958		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:241622318C>T	ENST00000407834.3	-	0	0					NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B							integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		AGGAGCTGGCCGGTTCCCACA	0.672																																																	0																																										SO:0001631	upstream_gene_variant	653437			BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263		2.37:g.241622318C>T	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_I	A4QPB9	Splice_Site	SNP	ENST00000407834.3	37	CCDS46560.1																																																																																				0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			
ATP5A1	498	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	43668204	43668204	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr18:43668204C>A	ENST00000398752.6	-	6	791	c.670G>T	c.(670-672)Gac>Tac	p.D224Y	ATP5A1_ENST00000282050.2_Missense_Mutation_p.D224Y|ATP5A1_ENST00000590665.1_Missense_Mutation_p.D202Y|ATP5A1_ENST00000593152.2_Missense_Mutation_p.D174Y	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	224					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.D224Y(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						ATGATTGTGTCAATAGCAATT	0.353																																																	1	Substitution - Missense(1)	kidney(1)											91.0	89.0	90.0					18																	43668204		2203	4300	6503	SO:0001583	missense	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	823	protein-coding gene	gene with protein product		164360	"""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2"", ""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"""	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.670G>T	18.37:g.43668204C>A	ENSP00000381736:p.Asp224Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387745	0.82902	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.82711	-1.64;-1.64	5.06	5.06	0.68205	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.044496	0.85682	D	0.000000	D	0.96454	0.8843	H	0.99985	5.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99406	1.0929	10	0.87932	D	0	-22.7919	18.4439	0.90677	0.0:1.0:0.0:0.0	.	224	P25705	ATPA_HUMAN	Y	224;224;174	ENSP00000282050:D224Y;ENSP00000381736:D224Y	ENSP00000282050:D224Y	D	-	1	0	ATP5A1	41922202	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.760000	0.85248	2.344000	0.79699	0.591000	0.81541	GAC		0.353	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1		NM_004046	
BCAS3	54828	broad.mit.edu;ucsc.edu	37	17	59155722	59155722	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr17:59155722A>G	ENST00000390652.5	+	22	2235	c.2204A>G	c.(2203-2205)cAt>cGt	p.H735R	BCAS3_ENST00000589222.1_Missense_Mutation_p.H720R|BCAS3_ENST00000588462.1_Missense_Mutation_p.H735R|BCAS3_ENST00000407086.3_Missense_Mutation_p.H720R|BCAS3_ENST00000585744.1_Missense_Mutation_p.H506R|BCAS3_ENST00000408905.3_Missense_Mutation_p.H720R|BCAS3_ENST00000588874.1_Missense_Mutation_p.H491R	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.H735R(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ACTGGACCCCATAGACGTCTG	0.448																																																	1	Substitution - Missense(1)	kidney(1)											119.0	113.0	115.0					17																	59155722		1917	4138	6055	SO:0001583	missense	54828			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2204A>G	17.37:g.59155722A>G	ENSP00000375067:p.His735Arg	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000390652.5	37	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.594166	0.86953	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	T;T;T	0.38240	1.16;1.15;1.18	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.60248	0.2254	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D	0.89917	0.996;1.0;0.96;0.991;0.96	D;D;D;D;D	0.83275	0.99;0.996;0.948;0.991;0.948	T	0.60535	-0.7244	10	0.46703	T	0.11	.	16.2071	0.82135	1.0:0.0:0.0:0.0	.	720;735;720;735;720	Q9H6U6-3;Q9H6U6-8;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;.;BCAS3_HUMAN;.	R	735;720;720	ENSP00000375067:H735R;ENSP00000385323:H720R;ENSP00000386173:H720R	ENSP00000375067:H735R	H	+	2	0	BCAS3	56510504	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.070000	0.93974	2.240000	0.73641	0.477000	0.44152	CAT		0.448	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1		NM_017679	
BEST1	7439	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	61730491	61730491	+	Intron	SNP	T	T	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:61730491T>C	ENST00000378043.4	+	10	2382				FTH1_ENST00000529191.1_Intron|BEST1_ENST00000301774.9_Missense_Mutation_p.L250P|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.L562P|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.L562P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						ACACTGGACCTACGCCCAGCA	0.567																																																	1	Substitution - Missense(1)	kidney(1)											86.0	76.0	79.0					11																	61730491		692	1591	2283	SO:0001627	intron_variant	7439			AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+126T>C	11.37:g.61730491T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.237219	0.39498	.	.	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97553	-0.53;-4.43	3.78	2.62	0.31277	.	.	.	.	.	D	0.89750	0.6805	N	0.08118	0	0.18873	N	0.999989	B	0.21225	0.053	B	0.14023	0.01	T	0.80881	-0.1184	8	.	.	.	.	5.9269	0.19118	0.0:0.2302:0.0:0.7698	.	562	O76090-3	.	P	250;562	ENSP00000301774:L250P;ENSP00000399709:L562P	.	L	+	2	0	BEST1	61487067	0.004000	0.15560	0.027000	0.17364	0.058000	0.15608	0.419000	0.21247	0.592000	0.29728	0.459000	0.35465	CTA		0.567	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1		NM_004183	
SAMD15	161394	broad.mit.edu	37	14	77844367	77844367	+	Silent	SNP	A	A	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr14:77844367A>G	ENST00000216471.4	+	1	892	c.606A>G	c.(604-606)gaA>gaG	p.E202E	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	202								p.E202E(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TGCAACATGAAGAGACAGGTC	0.468																																																	1	Substitution - coding silent(1)	kidney(1)											59.0	65.0	63.0					14																	77844367		2203	4300	6503	SO:0001819	synonymous_variant	0			AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.606A>G	14.37:g.77844367A>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																				0.468	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2		NM_001010860	
CCDC170	80129	broad.mit.edu;hgsc.bcm.edu	37	6	151894314	151894314	+	Silent	SNP	G	G	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr6:151894314G>A	ENST00000239374.7	+	6	879	c.780G>A	c.(778-780)ctG>ctA	p.L260L	CCDC170_ENST00000367290.5_Silent_p.L260L	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	260								p.L260L(1)									TTTAGGACCTGCTCAGTGCTG	0.443																																																	1	Substitution - coding silent(1)	kidney(1)											51.0	51.0	51.0					6																	151894314		1862	4107	5969	SO:0001819	synonymous_variant	0			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.780G>A	6.37:g.151894314G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	37	CCDS43515.1																																																																																				0.443	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2		NM_025059	
CHRNA2	1135	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	27321118	27321118	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr8:27321118C>G	ENST00000520933.2	-	5	995	c.842G>C	c.(841-843)tGc>tCc	p.C281S	CHRNA2_ENST00000240132.2_Missense_Mutation_p.C266S|CHRNA2_ENST00000407991.1_Missense_Mutation_p.C281S			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	281					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.C281S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	CACAGTGAGGCAGGAGATGAG	0.602																																																	1	Substitution - Missense(1)	kidney(1)											251.0	201.0	218.0					8																	27321118		2203	4300	6503	SO:0001583	missense	1135			U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.842G>C	8.37:g.27321118C>G	ENSP00000429616:p.Cys281Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.582299	0.65992	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	D;D;D	0.85556	-2.0;-2.0;-2.0	4.97	4.09	0.47781	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.042710	0.85682	D	0.000000	D	0.84606	0.5509	L	0.35793	1.09	0.80722	D	1	P;P	0.51791	0.948;0.889	P;P	0.55667	0.781;0.628	T	0.82257	-0.0547	10	0.30078	T	0.28	.	12.4368	0.55604	0.169:0.831:0.0:0.0	.	266;281	B4DK19;Q15822	.;ACHA2_HUMAN	S	281;281;266	ENSP00000385026:C281S;ENSP00000429616:C281S;ENSP00000240132:C266S	ENSP00000240132:C266S	C	-	2	0	CHRNA2	27377035	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.802000	0.62539	1.295000	0.44724	0.561000	0.74099	TGC		0.602	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			
CHST15	51363	hgsc.bcm.edu	37	10	125780753	125780753	+	Intron	DEL	G	G	-	rs528840982|rs398015013|rs5788645|rs550185991	byFrequency	TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr10:125780753delG	ENST00000346248.5	-	6	1990				CHST15_ENST00000421115.1_Frame_Shift_Del_p.R456fs|CHST15_ENST00000435907.1_Intron	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						CGGGGGGTACGGGGGGGGGGG	0.542													|||unknown(HR)	4042	0.807109	0.764	0.8429	5008	,	,		9633	0.874		0.829	False		,,,				2504	0.7485																0													5.0	5.0	5.0					10																	125780753		1998	3907	5905	SO:0001627	intron_variant	51363			AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1347+18C>-	10.37:g.125780753delG		Somatic		WXS	Illumina HiSeq	Phase_I	O60338|O60474|Q86VM4	Frame_Shift_Del	DEL	ENST00000346248.5	37	CCDS7638.1																																																																																				0.542	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1		NM_015892	
COL6A3	1293	broad.mit.edu	37	2	238280926	238280926	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:238280926C>T	ENST00000295550.4	-	9	4186	c.3734G>A	c.(3733-3735)gGg>gAg	p.G1245E	COL6A3_ENST00000409809.1_Missense_Mutation_p.G1039E|COL6A3_ENST00000353578.4_Missense_Mutation_p.G1039E|COL6A3_ENST00000346358.4_Missense_Mutation_p.G1045E|COL6A3_ENST00000392003.2_Missense_Mutation_p.G838E|COL6A3_ENST00000472056.1_Missense_Mutation_p.G638E|COL6A3_ENST00000392004.3_Missense_Mutation_p.G1039E|COL6A3_ENST00000347401.3_Missense_Mutation_p.G1044E	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1245	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G1245E(1)|p.G1039E(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GAACTCAGGCCCGGCACTTTG	0.552																																																	2	Substitution - Missense(2)	kidney(2)											69.0	65.0	66.0					2																	238280926		2203	4300	6503	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.3734G>A	2.37:g.238280926C>T	ENSP00000295550:p.Gly1245Glu	Somatic		WXS	Illumina GAIIx	Phase_I	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	8.644	0.896648	0.17686	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003	T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.58	1.13	0.20643	von Willebrand factor, type A (3);	0.980128	0.08308	N	0.965873	T	0.65460	0.2693	M	0.88181	2.935	0.09310	N	1	D;B;B;P;B	0.55800	0.973;0.146;0.075;0.868;0.096	P;B;B;P;B	0.60012	0.867;0.102;0.219;0.572;0.129	T	0.53422	-0.8441	10	0.72032	D	0.01	.	10.4231	0.44363	0.2195:0.3699:0.4106:0.0	.	638;838;1039;1039;1245	E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;CO6A3_HUMAN	E	1245;1044;1039;638;1039;1045;1039;838	ENSP00000295550:G1245E;ENSP00000315609:G1044E;ENSP00000315873:G1039E;ENSP00000418285:G638E;ENSP00000386844:G1039E;ENSP00000295546:G1045E;ENSP00000375861:G1039E;ENSP00000375860:G838E	ENSP00000295550:G1245E	G	-	2	0	COL6A3	237945665	0.000000	0.05858	0.002000	0.10522	0.279000	0.26890	0.098000	0.15189	0.284000	0.22305	-0.211000	0.12701	GGG		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2		NM_004369	
CRISPLD1	83690	broad.mit.edu;ucsc.edu	37	8	75927084	75927084	+	Missense_Mutation	SNP	C	C	T	rs566911502		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr8:75927084C>T	ENST00000262207.4	+	6	1132	c.664C>T	c.(664-666)Cgg>Tgg	p.R222W	CRISPLD1_ENST00000517786.1_Missense_Mutation_p.R36W|CRISPLD1_ENST00000523524.1_Missense_Mutation_p.R34W	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	222					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)		p.R222W(2)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			CAAACATGGGCGGCCCTGTTC	0.423																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											52.0	48.0	50.0					8																	75927084		2203	4300	6503	SO:0001583	missense	83690			AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.664C>T	8.37:g.75927084C>T	ENSP00000262207:p.Arg222Trp	Somatic		WXS	Illumina GAIIx	Phase_I	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	37	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.702661	0.68501	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	T;T;D	0.83250	0.2;-1.34;-1.7	4.6	3.69	0.42338	.	0.171361	0.46442	D	0.000284	T	0.79747	0.4499	L	0.49126	1.545	0.38547	D	0.949369	D;P	0.56968	0.978;0.903	B;B	0.43623	0.425;0.2	T	0.83052	-0.0152	10	0.72032	D	0.01	.	13.595	0.61984	0.1616:0.8384:0.0:0.0	.	36;222	B7Z929;Q9H336	.;CRLD1_HUMAN	W	222;34;36	ENSP00000262207:R222W;ENSP00000430105:R34W;ENSP00000429746:R36W	ENSP00000262207:R222W	R	+	1	2	CRISPLD1	76089639	0.107000	0.21998	0.873000	0.34254	0.895000	0.52256	1.508000	0.35769	1.085000	0.41206	0.460000	0.39030	CGG		0.423	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1		NM_031461	
CROCCP2	84809	broad.mit.edu	37	1	16952952	16952952	+	lincRNA	SNP	G	G	A	rs1762946	byFrequency	TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr1:16952952G>A	ENST00000412962.1	-	0	664							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											TCTGCCCTCAGCTTGGTCACG	0.622																																																	0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16952952G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.622	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
CYP4B1	1580	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	47279221	47279221	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr1:47279221C>T	ENST00000271153.4	+	5	599	c.563C>T	c.(562-564)gCg>gTg	p.A188V	CYP4B1_ENST00000371923.4_Missense_Mutation_p.A188V|CYP4B1_ENST00000452782.2_Missense_Mutation_p.A25V|CYP4B1_ENST00000371919.4_Missense_Mutation_p.A173V			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	188					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.A188V(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	GGTCACATGGCGCTGAACACA	0.572																																																	1	Substitution - Missense(1)	kidney(1)											111.0	107.0	108.0					1																	47279221		2203	4300	6503	SO:0001583	missense	1580			BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.563C>T	1.37:g.47279221C>T	ENSP00000271153:p.Ala188Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	37	CCDS542.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.753981	0.31046	.	.	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000526297;ENST00000452782;ENST00000468637	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	5.21	3.35	0.38373	.	0.107189	0.64402	N	0.000004	T	0.65995	0.2745	M	0.71581	2.175	0.34116	D	0.663558	B;B;B;B	0.27559	0.181;0.1;0.043;0.112	B;B;B;B	0.31101	0.016;0.098;0.052;0.124	T	0.72877	-0.4159	10	0.87932	D	0	.	11.9378	0.52884	0.0:0.8575:0.0:0.1425	.	25;173;188;188	E7EME6;Q8IZB0;P13584-2;P13584	.;.;.;CP4B1_HUMAN	V	188;188;173;25;25;25	ENSP00000360991:A188V;ENSP00000271153:A188V;ENSP00000360987:A173V;ENSP00000438995:A25V;ENSP00000400413:A25V;ENSP00000437670:A25V	ENSP00000271153:A188V	A	+	2	0	CYP4B1	47051808	0.998000	0.40836	0.584000	0.28653	0.003000	0.03518	3.805000	0.55575	0.610000	0.30035	-0.967000	0.02615	GCG		0.572	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1		NM_000779	
DDAH1	23576	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	85817252	85817252	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr1:85817252A>C	ENST00000284031.8	-	3	508	c.414T>G	c.(412-414)ttT>ttG	p.F138L	RP11-131L23.1_ENST00000426125.1_RNA|DDAH1_ENST00000542148.1_Missense_Mutation_p.F38L|DDAH1_ENST00000539042.1_Missense_Mutation_p.F138L|DDAH1_ENST00000426972.3_Missense_Mutation_p.F45L|RP11-131L23.1_ENST00000427819.1_RNA|DDAH1_ENST00000483110.1_5'UTR|DDAH1_ENST00000535924.2_Missense_Mutation_p.F35L	NM_012137.3	NP_036269.1	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1	138					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of angiogenesis (GO:0045766)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of systemic arterial blood pressure (GO:0003073)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)|metal ion binding (GO:0046872)	p.F138L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|skin(1)	5				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	GGCCCACAAAAAATTCTCTGC	0.388																																																	1	Substitution - Missense(1)	kidney(1)											106.0	102.0	103.0					1																	85817252		2203	4300	6503	SO:0001583	missense	23576			AB001915	CCDS705.1, CCDS44170.1	1p22	2008-02-05			ENSG00000153904	ENSG00000153904	3.5.3.18		2715	protein-coding gene	gene with protein product		604743				9874257	Standard	NM_012137		Approved	DDAH	uc001dlb.3	O94760	OTTHUMG00000010578	ENST00000284031.8:c.414T>G	1.37:g.85817252A>C	ENSP00000284031:p.Phe138Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5HYC8|Q86XK5	Missense_Mutation	SNP	ENST00000284031.8	37	CCDS705.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.875336	0.91664	.	.	ENSG00000153904	ENST00000284031;ENST00000539042;ENST00000535924;ENST00000426972;ENST00000542148	.	.	.	5.41	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.51618	0.1685	M	0.61703	1.905	0.80722	D	1	D;P	0.69078	0.997;0.639	D;B	0.65140	0.932;0.348	T	0.55988	-0.8053	9	0.14656	T	0.56	-11.8157	5.3862	0.16220	0.7553:0.0:0.2447:0.0	.	38;138	B4DYP1;O94760	.;DDAH1_HUMAN	L	138;138;35;45;38	.	ENSP00000284031:F138L	F	-	3	2	DDAH1	85589840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.465000	0.45075	2.049000	0.60858	0.533000	0.62120	TTT		0.388	DDAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029189.1			
DCAF6	55827	broad.mit.edu;ucsc.edu	37	1	168034953	168034953	+	Silent	SNP	A	A	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr1:168034953A>T	ENST00000312263.6	+	16	2496	c.2292A>T	c.(2290-2292)gtA>gtT	p.V764V	DCAF6_ENST00000432587.2_Silent_p.V824V|DCAF6_ENST00000367840.3_Silent_p.V855V|DCAF6_ENST00000367843.3_Silent_p.V784V	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	764					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.V784V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						ATCATGTGGTAAACTGCCTGC	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											77.0	73.0	74.0					1																	168034953		2203	4300	6503	SO:0001819	synonymous_variant	55827			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.2292A>T	1.37:g.168034953A>T		Somatic		WXS	Illumina GAIIx	Phase_I	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Silent	SNP	ENST00000312263.6	37	CCDS30933.1																																																																																				0.418	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2		NM_018442	
EPS8L1	54869	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	55597327	55597327	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr19:55597327C>T	ENST00000201647.6	+	15	1560	c.1504C>T	c.(1504-1506)Cgg>Tgg	p.R502W	EPS8L1_ENST00000540810.1_Missense_Mutation_p.R438W|EPS8L1_ENST00000588359.1_Missense_Mutation_p.R188W|EPS8L1_ENST00000586329.1_Missense_Mutation_p.R516W|EPS8L1_ENST00000245618.5_Missense_Mutation_p.R375W	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	502	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)	p.R516W(1)|p.R502W(1)|p.R375W(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		GGTCAAGCAGCGGGACGTACT	0.562																																					Ovarian(149;255 1863 3636 27051 29647)												3	Substitution - Missense(3)	kidney(3)											69.0	67.0	68.0					19																	55597327		2203	4300	6503	SO:0001583	missense	54869			AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1504C>T	19.37:g.55597327C>T	ENSP00000201647:p.Arg502Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932993	0.34096	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.48201	0.82;0.82;0.82	4.43	-3.32	0.04973	Src homology-3 domain (4);	0.264843	0.35615	N	0.003083	T	0.22859	0.0552	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.21147	0.003;0.012;0.052;0.006	B;B;B;B	0.13407	0.001;0.006;0.009;0.003	T	0.06075	-1.0847	10	0.56958	D	0.05	-7.7961	3.2809	0.06915	0.2434:0.3166:0.3502:0.0898	.	516;281;375;502	Q8TE68-3;Q8TE68-4;Q8TE68-2;Q8TE68	.;.;.;ES8L1_HUMAN	W	516;502;438;375;188	ENSP00000201647:R502W;ENSP00000437541:R438W;ENSP00000245618:R375W	ENSP00000201647:R502W	R	+	1	2	EPS8L1	60289139	0.008000	0.16893	0.005000	0.12908	0.015000	0.08874	0.375000	0.20518	-0.218000	0.10018	-0.466000	0.05196	CGG		0.562	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1		NM_017729	
ERBB2	2064	broad.mit.edu	37	17	37883729	37883729	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr17:37883729A>G	ENST00000269571.5	+	26	3500	c.3341A>G	c.(3340-3342)gAg>gGg	p.E1114G	ERBB2_ENST00000540147.1_Missense_Mutation_p.E1084G|MIEN1_ENST00000474210.1_5'Flank|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000541774.1_Missense_Mutation_p.E1099G|ERBB2_ENST00000445658.2_Missense_Mutation_p.E838G|ERBB2_ENST00000584450.1_Intron|ERBB2_ENST00000584601.1_Missense_Mutation_p.E1084G|ERBB2_ENST00000406381.2_Missense_Mutation_p.E1084G			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	1114					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.E1114G(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CGGTACAGTGAGGACCCCACA	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																														Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	1	Substitution - Missense(1)	kidney(1)											62.0	64.0	63.0					17																	37883729		2203	4300	6503	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.3341A>G	17.37:g.37883729A>G	ENSP00000269571:p.Glu1114Gly	Somatic		WXS	Illumina GAIIx	Phase_I	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.000737	0.54254	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.77229	-1.08;-1.08;-1.06;-1.08;-1.08	5.2	4.1	0.47936	.	.	.	.	.	T	0.74291	0.3697	L	0.51422	1.61	0.80722	D	1	P;P;P	0.47910	0.61;0.902;0.61	B;P;B	0.46543	0.219;0.52;0.219	T	0.71155	-0.4675	9	0.39692	T	0.17	.	9.748	0.40459	0.8457:0.0:0.0:0.1543	.	838;1099;1114	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	G	1084;1099;838;1114;1084	ENSP00000385185:E1084G;ENSP00000446466:E1099G;ENSP00000404047:E838G;ENSP00000269571:E1114G;ENSP00000443562:E1084G	ENSP00000269571:E1114G	E	+	2	0	ERBB2	35137255	1.000000	0.71417	0.994000	0.49952	0.935000	0.57460	6.076000	0.71267	0.772000	0.33382	0.459000	0.35465	GAG		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			
GALNT15	117248	broad.mit.edu;ucsc.edu	37	3	16237362	16237362	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr3:16237362A>G	ENST00000339732.5	+	2	1138	c.635A>G	c.(634-636)cAc>cGc	p.H212R	GALNT15_ENST00000437509.1_Missense_Mutation_p.H212R	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	212	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.H212R(1)									CGGACTGTACACAGCATCCTC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											104.0	78.0	86.0					3																	16237362		2203	4300	6503	SO:0001583	missense	117248			AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.635A>G	3.37:g.16237362A>G	ENSP00000344260:p.His212Arg	Somatic		WXS	Illumina GAIIx	Phase_I	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.569588	0.86439	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.60548	0.18;0.18	4.88	4.88	0.63580	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.71978	0.3404	L	0.60845	1.875	0.58432	D	0.999992	D	0.89917	1.0	D	0.80764	0.994	T	0.75522	-0.3288	10	0.87932	D	0	.	14.5169	0.67826	1.0:0.0:0.0:0.0	.	212	Q8N3T1	GLTL2_HUMAN	R	212	ENSP00000344260:H212R;ENSP00000395873:H212R	ENSP00000344260:H212R	H	+	2	0	GALNTL2	16212366	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.476000	0.81055	1.831000	0.53308	0.454000	0.30748	CAC		0.607	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2		NM_054110	
IQCG	84223	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	197652965	197652965	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr3:197652965C>A	ENST00000265239.6	-	7	1080	c.656G>T	c.(655-657)gGa>gTa	p.G219V	IQCG_ENST00000453254.1_Missense_Mutation_p.G219V|IQCG_ENST00000455191.1_Missense_Mutation_p.G219V	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	219						extracellular vesicular exosome (GO:0070062)		p.G219V(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CTGTTTTCTTCCTTTTTCCTC	0.368																																																	1	Substitution - Missense(1)	kidney(1)											198.0	177.0	184.0					3																	197652965		2203	4298	6501	SO:0001583	missense	84223			AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.656G>T	3.37:g.197652965C>A	ENSP00000265239:p.Gly219Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502186	0.64298	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254	T;T;T	0.48836	0.8;0.8;0.86	4.44	4.44	0.53790	.	0.072571	0.53938	D	0.000054	T	0.66655	0.2811	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.974	T	0.65105	-0.6249	10	0.21014	T	0.42	-18.7748	13.0046	0.58696	0.0:1.0:0.0:0.0	.	219;219	C9JKX8;Q9H095	.;IQCG_HUMAN	V	219	ENSP00000265239:G219V;ENSP00000407736:G219V;ENSP00000389897:G219V	ENSP00000265239:G219V	G	-	2	0	IQCG	199137362	1.000000	0.71417	0.989000	0.46669	0.922000	0.55478	3.745000	0.55119	2.202000	0.70862	0.650000	0.86243	GGA		0.368	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1		NM_032263	
KRTAP5-7	440050	broad.mit.edu	37	11	71238705	71238705	+	Missense_Mutation	SNP	G	G	A	rs536797652		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:71238705G>A	ENST00000398536.4	+	1	393	c.359G>A	c.(358-360)tGc>tAc	p.C120Y		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	120	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.C120Y(2)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						tgtaagccctgctgctgccag	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		20154	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)											129.0	139.0	136.0					11																	71238705		2200	4294	6494	SO:0001583	missense	440050			AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.359G>A	11.37:g.71238705G>A	ENSP00000417330:p.Cys120Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	4.462	0.085611	0.08583	.	.	ENSG00000244411	ENST00000398536	T	0.01304	5.03	1.87	1.87	0.25490	.	.	.	.	.	T	0.01421	0.0046	L	0.60455	1.87	0.26143	N	0.980242	B	0.12630	0.006	B	0.08055	0.003	T	0.51733	-0.8668	9	0.02654	T	1	.	4.3831	0.11304	0.201:0.0:0.799:0.0	.	120	Q6L8G8	KRA57_HUMAN	Y	120	ENSP00000417330:C120Y	ENSP00000417330:C120Y	C	+	2	0	KRTAP5-7	70916353	0.718000	0.27976	0.999000	0.59377	0.075000	0.17131	2.143000	0.42187	1.367000	0.46095	0.289000	0.19496	TGC		0.607	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			
ANKRD66	100287718	broad.mit.edu;ucsc.edu	37	6	46721623	46721623	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr6:46721623G>A	ENST00000565422.1	+	4	498	c.493G>A	c.(493-495)Gga>Aga	p.G165R	ANKRD66_ENST00000536046.1_Missense_Mutation_p.G136R	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	165								p.G165R(2)									TGACTTCTTTGGAGACACACC	0.478																																																	2	Substitution - Missense(2)	kidney(2)											60.0	53.0	55.0					6																	46721623		692	1591	2283	SO:0001583	missense	0			AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.493G>A	6.37:g.46721623G>A	ENSP00000454770:p.Gly165Arg	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000565422.1	37	CCDS59024.1																																																																																				0.478	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1		NM_001162435	
LINC01257	116437	broad.mit.edu	37	12	131696762	131696762	+	lincRNA	DEL	G	G	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr12:131696762delG	ENST00000376678.2	+	0	1759					NR_026670.2																						TCCTGGCACTGCTGGACCTGT	0.542																																																	0																																												116437																															12.37:g.131696762delG		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000376678.2	37																																																																																					0.542	RP11-638F5.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000399382.1			
LRRC8E	80131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	7964495	7964495	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr19:7964495T>C	ENST00000306708.6	+	3	1189	c.1088T>C	c.(1087-1089)tTc>tCc	p.F363S	AC010336.1_ENST00000539278.1_3'UTR|RN7SL115P_ENST00000392196.5_RNA	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	363					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F363S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						AAGAATGACTTCGCCTTCATG	0.582																																																	1	Substitution - Missense(1)	kidney(1)											107.0	80.0	89.0					19																	7964495		2203	4300	6503	SO:0001583	missense	80131				CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1088T>C	19.37:g.7964495T>C	ENSP00000306524:p.Phe363Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517089	0.64634	.	.	ENSG00000171017	ENST00000306708	T	0.29397	1.57	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.55257	0.1909	M	0.80616	2.505	0.58432	D	0.999998	D	0.76494	0.999	D	0.68621	0.959	T	0.61603	-0.7029	10	0.87932	D	0	.	12.5165	0.56036	0.0:0.0:0.0:1.0	.	363	Q6NSJ5	LRC8E_HUMAN	S	363	ENSP00000306524:F363S	ENSP00000306524:F363S	F	+	2	0	LRRC8E	7870495	1.000000	0.71417	0.934000	0.37439	0.755000	0.42902	7.863000	0.87023	2.060000	0.61445	0.454000	0.30748	TTC		0.582	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1		NM_025061	
MSX2	4488	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	174156377	174156377	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr5:174156377A>T	ENST00000239243.6	+	2	722	c.595A>T	c.(595-597)Aga>Tga	p.R199*		NM_002449.4	NP_002440.2	P35548	MSX2_HUMAN	msh homeobox 2	199					activation of meiosis (GO:0090427)|anagen (GO:0042640)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone trabecula formation (GO:0060346)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte development (GO:0002063)|cranial suture morphogenesis (GO:0060363)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|enamel mineralization (GO:0070166)|endochondral bone growth (GO:0003416)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|frontal suture morphogenesis (GO:0060364)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of catagen (GO:0051795)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of osteoblast differentiation (GO:0045669)|signal transduction involved in regulation of gene expression (GO:0023019)|wound healing, spreading of epidermal cells (GO:0035313)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 (GO:0000982)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.R199*(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAAGGCGAAAAGACTGCAGGA	0.552																																																	1	Substitution - Nonsense(1)	kidney(1)											64.0	64.0	64.0					5																	174156377		2203	4300	6503	SO:0001587	stop_gained	4488			D26145	CCDS4392.1	5q35.2	2011-06-20	2006-11-21		ENSG00000120149	ENSG00000120149		"""Homeoboxes / ANTP class : NKL subclass"""	7392	protein-coding gene	gene with protein product	"""craniosynostosis, type 2"""	123101	"""msh (Drosophila) homeo box homolog 2"", ""parietal foramina 1"", ""msh homeobox homolog 2 (Drosophila)"""	PFM1		8668339, 8786091	Standard	XM_006714868		Approved	CRS2, FPP, HOX8, MSH, PFM	uc003mcy.3	P35548	OTTHUMG00000130556	ENST00000239243.6:c.595A>T	5.37:g.174156377A>T	ENSP00000239243:p.Arg199*	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQN1|Q53XM4|Q9UD60	Nonsense_Mutation	SNP	ENST00000239243.6	37	CCDS4392.1	.	.	.	.	.	.	.	.	.	.	A	36	5.624732	0.96660	.	.	ENSG00000120149	ENST00000239243	.	.	.	5.83	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2529	12.7135	0.57102	0.8628:0.1372:0.0:0.0	.	.	.	.	X	199	.	ENSP00000239243:R199X	R	+	1	2	MSX2	174088983	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.741000	0.55090	2.229000	0.72834	0.482000	0.46254	AGA		0.552	MSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252981.3			
MUC2	4583	hgsc.bcm.edu	37	11	1092841	1092841	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:1092841delG	ENST00000441003.2	+	30	4687	c.4660delG	c.(4660-4662)ggcfs	p.G1554fs	MUC2_ENST00000359061.5_Frame_Shift_Del_p.G1555fs|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AACACCCACCGGCACACAGAC	0.632																																																	0													79.0	103.0	94.0					11																	1092841		1868	3445	5313	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.4660delG	11.37:g.1092841delG	ENSP00000415183:p.Gly1554fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2		NM_002457	
MUC4	4585	broad.mit.edu	37	3	195505855	195505855	+	Missense_Mutation	SNP	G	G	T	rs201422998		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr3:195505855G>T	ENST00000463781.3	-	2	13055	c.12596C>A	c.(12595-12597)tCc>tAc	p.S4199Y	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S4199Y	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.S4199Y(6)		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)		GGATGCTGAGGAAGTGTCGGT	0.597																																																	6	Substitution - Missense(6)	kidney(4)|endometrium(2)																																								SO:0001583	missense	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.12596C>A	3.37:g.195505855G>T	ENSP00000417498:p.Ser4199Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.831	-0.469745	0.04445	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.26;1.38	.	.	.	.	.	.	.	.	T	0.36826	0.0981	N	0.19112	0.55	0.19300	N	0.999978	D	0.57571	0.98	D	0.66847	0.947	T	0.18241	-1.0343	7	.	.	.	.	6.6097	0.22745	2.0E-4:0.0:0.9998:0.0	.	4071	E7ESK3	.	Y	4199	ENSP00000417498:S4199Y;ENSP00000420243:S4199Y	.	S	-	2	0	MUC4	196990634	0.001000	0.12720	0.030000	0.17652	0.035000	0.12851	-0.256000	0.08757	0.452000	0.26830	0.074000	0.15403	TCC		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
NFATC4	4776	hgsc.bcm.edu	37	14	24845849	24845850	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr14:24845849_24845850insC	ENST00000250373.4	+	9	2547_2548	c.2406_2407insC	c.(2407-2409)ctgfs	p.L803fs	NFATC4_ENST00000553469.1_Intron|NFATC4_ENST00000554050.1_Intron|NFATC4_ENST00000557451.1_Frame_Shift_Ins_p.L733fs|NFATC4_ENST00000554344.1_Frame_Shift_Ins_p.L733fs|NFATC4_ENST00000556279.1_Frame_Shift_Ins_p.L835fs|NFATC4_ENST00000555802.1_Frame_Shift_Ins_p.L91fs|NFATC4_ENST00000555453.1_Frame_Shift_Ins_p.L791fs|NFATC4_ENST00000554591.1_Intron|NFATC4_ENST00000422617.3_Frame_Shift_Ins_p.L791fs|NFATC4_ENST00000555393.1_Frame_Shift_Ins_p.L91fs|NFATC4_ENST00000413692.2_Frame_Shift_Ins_p.L866fs|NFATC4_ENST00000557767.1_Intron|NFATC4_ENST00000553879.1_Frame_Shift_Ins_p.L733fs|NFATC4_ENST00000555590.1_Frame_Shift_Ins_p.L816fs|NFATC4_ENST00000539237.2_Frame_Shift_Ins_p.L835fs|NFATC4_ENST00000554661.1_Intron|NFATC4_ENST00000554473.1_Intron|NFATC4_ENST00000556759.1_Frame_Shift_Ins_p.L338fs|NFATC4_ENST00000556169.1_Intron|NFATC4_ENST00000555167.1_Frame_Shift_Ins_p.L338fs|NFATC4_ENST00000554966.1_Intron|NFATC4_ENST00000553708.1_Frame_Shift_Ins_p.L803fs|NFATC4_ENST00000424781.2_Frame_Shift_Ins_p.L816fs	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	803	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		TCTCCCTGGGGCTGCCATTCTC	0.644																																																	0																																										SO:0001589	frameshift_variant	4776			BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2407dupC	14.37:g.24845850_24845850dupC	ENSP00000250373:p.Leu803fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Frame_Shift_Ins	INS	ENST00000250373.4	37	CCDS9629.1																																																																																				0.644	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6		NM_004554	
NRXN1	9378	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	50723141	50723141	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:50723141A>C	ENST00000406316.2	-	15	4448	c.2972T>G	c.(2971-2973)gTg>gGg	p.V991G	NRXN1_ENST00000405472.3_Missense_Mutation_p.V983G|NRXN1_ENST00000401669.2_Missense_Mutation_p.V991G|NRXN1_ENST00000406859.3_Missense_Mutation_p.V991G|NRXN1_ENST00000401710.1_5'UTR|NRXN1_ENST00000402717.3_Missense_Mutation_p.V983G|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000404971.1_Missense_Mutation_p.V1031G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	991	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.V991G(1)|p.V1031G(1)|p.V1032G(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TGATATCATCACGTTGTGCCA	0.438																																																	3	Substitution - Missense(3)	kidney(3)											168.0	154.0	159.0					2																	50723141		2054	4201	6255	SO:0001583	missense	9378			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2972T>G	2.37:g.50723141A>C	ENSP00000384311:p.Val991Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446630	0.84101	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	D	0.95535	0.8549	H	0.96489	3.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96933	0.9682	10	0.87932	D	0	.	15.0872	0.72165	1.0:0.0:0.0:0.0	.	1031;991;983	Q9ULB1-3;F8WB18;A7E294	.;.;.	G	1031;991;983;991;1032;983;991	ENSP00000385142:V1031G;ENSP00000384311:V991G;ENSP00000434015:V983G;ENSP00000385017:V991G;ENSP00000385434:V983G;ENSP00000385681:V991G	ENSP00000385017:V991G	V	-	2	0	NRXN1	50576645	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	9.080000	0.94040	2.204000	0.70986	0.533000	0.62120	GTG		0.438	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			
NUDT21	11051	hgsc.bcm.edu	37	16	56485075	56485076	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr16:56485075_56485076insC	ENST00000300291.5	-	1	211_212	c.39_40insG	c.(37-42)tggcccfs	p.P14fs	OGFOD1_ENST00000566157.1_5'Flank|OGFOD1_ENST00000568397.1_5'Flank	NM_007006.2	NP_008937.1	O43809	CPSF5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 21	14	Necessary for RNA-binding.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	AU-rich element binding (GO:0017091)|histone deacetylase binding (GO:0042826)|hydrolase activity (GO:0016787)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)	7						ACCCCCCGGGGCCAGCCGGTCT	0.658																																																	0																																										SO:0001589	frameshift_variant	11051			AJ001810	CCDS10760.1	16q12.2	2013-06-18	2005-07-11	2005-07-11	ENSG00000167005	ENSG00000167005		"""Nudix motif containing"""	13870	protein-coding gene	gene with protein product	"""cleavage factor Im complex 25 kDa subunit"""	604978	"""cleavage and polyadenylation specific factor 5, 25 kDa"", ""cleavage and polyadenylation specific factor 5, 25 kD subunit"""	CPSF5		9659921	Standard	NM_007006		Approved	CFIM25	uc002eja.3	O43809	OTTHUMG00000133240	ENST00000300291.5:c.40dupG	16.37:g.56485077_56485077dupC	ENSP00000300291:p.Pro14fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IB85|Q6NE84	Frame_Shift_Ins	INS	ENST00000300291.5	37	CCDS10760.1																																																																																				0.658	NUDT21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256980.3		NM_007006	
PMS2	5395	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	6042192	6042192	+	Silent	SNP	A	A	G	rs35650314		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr7:6042192A>G	ENST00000265849.7	-	5	534	c.429T>C	c.(427-429)atT>atC	p.I143I	PMS2_ENST00000382321.4_Silent_p.I143I|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Silent_p.I143I|PMS2_ENST00000441476.2_Silent_p.I37I|Y_RNA_ENST00000365120.1_RNA	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	143					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.I143I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TTTTCTGGATAATTTTCCCAT	0.502			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	1	Substitution - coding silent(1)	kidney(1)											108.0	113.0	111.0					7																	6042192		2203	4300	6503	SO:0001819	synonymous_variant	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.429T>C	7.37:g.6042192A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.502	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3		NM_000535	
PODXL2	50512	hgsc.bcm.edu;ucsc.edu	37	3	127390442	127390442	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr3:127390442delA	ENST00000342480.6	+	7	1630	c.1591delA	c.(1591-1593)aagfs	p.K531fs	ABTB1_ENST00000232744.8_5'Flank|ABTB1_ENST00000453791.2_5'Flank|ABTB1_ENST00000468137.1_5'Flank|ABTB1_ENST00000393363.3_5'Flank	NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	531					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						CCGGCTGCCCAAGCTCAAGCA	0.617																																																	0													72.0	63.0	66.0					3																	127390442		2203	4300	6503	SO:0001589	frameshift_variant	50512			AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.1591delA	3.37:g.127390442delA	ENSP00000345359:p.Lys531fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6UVY4|Q8WUV6	Frame_Shift_Del	DEL	ENST00000342480.6	37	CCDS3044.1																																																																																				0.617	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1		NM_015720	
PRDM6	93166	broad.mit.edu	37	5	122425712	122425712	+	Start_Codon_Del	DEL	G	G	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr5:122425712delG	ENST00000407847.4	+	0	417				AC106786.1_ENST00000458103.2_RNA|AC106786.1_ENST00000442777.2_RNA	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6						negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						CGCCGGACATGCTGAAGCCCG	0.692																																																	0													3.0	4.0	4.0					5																	122425712		578	1403	1981	SO:0001582	initiator_codon_variant	93166			AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469		5.37:g.122425712delG		Somatic		WXS	Illumina GAIIx	Phase_I	B5MCJ4|Q9NQW9	Frame_Shift_Del	DEL	ENST00000407847.4	37	CCDS47259.1																																																																																				0.692	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2		XM_049619	
RGL3	57139	broad.mit.edu	37	19	11529441	11529441	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr19:11529441delC	ENST00000380456.3	-	2	116	c.53delG	c.(52-54)ggtfs	p.G18fs	RGL3_ENST00000393423.3_Frame_Shift_Del_p.G18fs	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	18					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						GGTCTCTTCACCCCAGTCCTG	0.731																																					GBM(174;751 2067 17998 27979 33959)												0													9.0	9.0	9.0					19																	11529441		2170	4264	6434	SO:0001589	frameshift_variant	57139			BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.53delG	19.37:g.11529441delC	ENSP00000369823:p.Gly18fs	Somatic		WXS	Illumina GAIIx	Phase_I	B5ME84|B7ZL22|Q0P6G0	Frame_Shift_Del	DEL	ENST00000380456.3	37	CCDS32910.1																																																																																				0.731	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3		XM_290867	
RGL4	266747	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	24034361	24034361	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr22:24034361G>T	ENST00000290691.5	+	1	1314	c.144G>T	c.(142-144)caG>caT	p.Q48H	KB-1572G7.2_ENST00000421064.1_RNA|AP000347.2_ENST00000417194.1_RNA|GUSBP11_ENST00000455485.1_RNA|RGL4_ENST00000401461.1_Intron	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	48					small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q48H(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						TGTATGGCCAGGTCTGCCCCT	0.637																																																	1	Substitution - Missense(1)	kidney(1)											101.0	94.0	96.0					22																	24034361		2203	4300	6503	SO:0001583	missense	266747				CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"""RalGDS related oncogene"""	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.144G>T	22.37:g.24034361G>T	ENSP00000290691:p.Gln48His	Somatic		WXS	Illumina HiSeq	Phase_I	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	37	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	g	13.42	2.230851	0.39399	.	.	ENSG00000159496	ENST00000290691;ENST00000382833;ENST00000423392	T;T	0.32515	1.64;1.45	1.72	1.72	0.24424	.	2.588180	0.03390	U	0.201772	T	0.36663	0.0975	L	0.27053	0.805	0.09310	N	1	D;P	0.59357	0.985;0.943	P;P	0.55667	0.769;0.781	T	0.40117	-0.9580	10	0.38643	T	0.18	.	9.4001	0.38426	0.0:0.0:1.0:0.0	.	48;48	E9PH87;Q8IZJ4	.;RGDSR_HUMAN	H	48	ENSP00000290691:Q48H;ENSP00000402142:Q48H	ENSP00000290691:Q48H	Q	+	3	2	RGL4	22364361	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.902000	0.04088	1.273000	0.44346	0.436000	0.28706	CAG		0.637	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1		NM_153615	
RGS3	5998	broad.mit.edu;ucsc.edu	37	9	116267783	116267783	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr9:116267783G>C	ENST00000374140.2	+	12	1168	c.959G>C	c.(958-960)cGa>cCa	p.R320P	RGS3_ENST00000343817.5_Missense_Mutation_p.R39P|RGS3_ENST00000374136.1_5'UTR|RGS3_ENST00000394646.3_Missense_Mutation_p.R39P|RGS3_ENST00000317613.6_Missense_Mutation_p.R208P|RGS3_ENST00000350696.5_Missense_Mutation_p.R320P	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	320	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R208P(1)|p.R320P(1)|p.R216P(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						TCTCCAGTTCGAGTCCAGGCC	0.562																																																	3	Substitution - Missense(3)	kidney(3)											148.0	106.0	120.0					9																	116267783		2203	4300	6503	SO:0001583	missense	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.959G>C	9.37:g.116267783G>C	ENSP00000363255:p.Arg320Pro	Somatic		WXS	Illumina GAIIx	Phase_I	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059400	0.93846	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646	T;T;T;T;T	0.27402	1.67;1.67;1.67;1.67;1.67	6.01	6.01	0.97437	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.58278	0.2111	M	0.75447	2.3	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.997;1.0;0.999;0.999	T	0.58858	-0.7562	10	0.87932	D	0	.	17.6771	0.88233	0.0:0.0:1.0:0.0	.	39;39;210;208;320	B3KUB2;P49796-4;B3KWG8;P49796-5;P49796	.;.;.;.;RGS3_HUMAN	P	320;320;208;39;39	ENSP00000363255:R320P;ENSP00000259406:R320P;ENSP00000312844:R208P;ENSP00000340284:R39P;ENSP00000378141:R39P	ENSP00000312844:R208P	R	+	2	0	RGS3	115307604	1.000000	0.71417	0.997000	0.53966	0.894000	0.52154	8.765000	0.91724	2.861000	0.98227	0.650000	0.86243	CGA		0.562	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3		NM_017790	
SCPEP1	59342	hgsc.bcm.edu;ucsc.edu	37	17	55072362	55072362	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr17:55072362delC	ENST00000262288.3	+	7	695	c.640delC	c.(640-642)cctfs	p.P214fs	SCPEP1_ENST00000571898.1_3'UTR	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	214					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					CTCCTGGGGACCTTACCTGTA	0.463																																																	0													205.0	164.0	178.0					17																	55072362		2203	4300	6503	SO:0001589	frameshift_variant	59342			AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.640delC	17.37:g.55072362delC	ENSP00000262288:p.Pro214fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q96A94|Q9H3F0	Frame_Shift_Del	DEL	ENST00000262288.3	37	CCDS11593.1																																																																																				0.463	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1		NM_021626	
SIRPG	55423	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	1616066	1616066	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr20:1616066A>T	ENST00000303415.3	-	4	992	c.928T>A	c.(928-930)Tgg>Agg	p.W310R	SIRPG_ENST00000381580.1_Missense_Mutation_p.W277R|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000216927.4_Intron|SIRPG_ENST00000381583.2_Intron|SIRPG_ENST00000344103.4_Intron|RP11-77C3.3_ENST00000437384.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	310	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.W310R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						CAGCTTGTCCAGTTGTAGGTA	0.547																																																	1	Substitution - Missense(1)	kidney(1)											226.0	179.0	195.0					20																	1616066		2203	4300	6503	SO:0001583	missense	55423			AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.928T>A	20.37:g.1616066A>T	ENSP00000305529:p.Trp310Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	6.990	0.552682	0.13374	.	.	ENSG00000089012	ENST00000381580;ENST00000303415	T;T	0.02709	4.19;4.19	1.6	-1.93	0.07594	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	2.650470	0.01169	N	0.006835	T	0.03136	0.0092	L	0.36672	1.1	0.09310	N	0.999999	B	0.22346	0.068	B	0.24394	0.053	T	0.43540	-0.9385	10	0.27082	T	0.32	.	4.9568	0.14046	0.4125:0.0:0.5875:0.0	.	310	Q9P1W8	SIRPG_HUMAN	R	277;310	ENSP00000370992:W277R;ENSP00000305529:W310R	ENSP00000305529:W310R	W	-	1	0	SIRPG	1564066	0.000000	0.05858	0.031000	0.17742	0.346000	0.29079	-0.026000	0.12392	-0.430000	0.07318	0.164000	0.16699	TGG		0.547	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2		NM_018556	
SYNPO	11346	hgsc.bcm.edu	37	5	150028961	150028962	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr5:150028961_150028962insC	ENST00000394243.1	+	3	2230_2231	c.1856_1857insC	c.(1855-1860)ggcagcfs	p.S620fs	SYNPO_ENST00000522122.1_Frame_Shift_Ins_p.S620fs|SYNPO_ENST00000519664.1_Frame_Shift_Ins_p.S376fs|SYNPO_ENST00000307662.4_Frame_Shift_Ins_p.S376fs	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	620					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCCGCCGGGGCAGCCGCAAAT	0.599																																																	0																																										SO:0001589	frameshift_variant	11346			AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.1857dupC	5.37:g.150028962_150028962dupC	ENSP00000377789:p.Ser620fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKZ8|D3DQG8|O15271|Q9UPX1	Frame_Shift_Ins	INS	ENST00000394243.1	37	CCDS54937.1																																																																																				0.599	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1		NM_007286	
SYT12	91683	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	66807536	66807536	+	Silent	SNP	G	G	A			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:66807536G>A	ENST00000393946.2	+	7	1645	c.483G>A	c.(481-483)gaG>gaA	p.E161E	SYT12_ENST00000527043.1_Silent_p.E161E|SYT12_ENST00000525457.1_Silent_p.E161E|SYT12_ENST00000526281.1_3'UTR			Q8IV01	SYT12_HUMAN	synaptotagmin XII	161						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)		p.E161E(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						TGAGCATGGAGTACGACACTG	0.627																																					Ovarian(65;2862 3307)												1	Substitution - coding silent(1)	kidney(1)											74.0	68.0	70.0					11																	66807536		2200	4295	6495	SO:0001819	synonymous_variant	91683			AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"""Synaptotagmins"""	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.483G>A	11.37:g.66807536G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000393946.2	37	CCDS8154.1																																																																																				0.627	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1		NM_177963	
TBC1D3G	654341	hgsc.bcm.edu	37	17	34746599	34746600	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr17:34746599_34746600insG	ENST00000330458.7	-	14	1640_1641	c.1484_1485insC	c.(1483-1485)gctfs	p.A495fs	TBC1D3G_ENST00000535592.1_Frame_Shift_Ins_p.A473fs|TBC1D3C_ENST00000451448.2_Intron|TBC1D3H_ENST00000455054.2_Frame_Shift_Ins_p.A495fs|TBC1D3H_ENST00000394359.3_Frame_Shift_Ins_p.A473fs|TBC1D3G_ENST00000535805.1_Frame_Shift_Ins_p.A415fs|TBC1D3H_ENST00000400684.4_Intron|TBC1D3C_ENST00000308078.7_Intron|TBC1D3H_ENST00000535446.1_Intron			Q6DHY5	TBC3G_HUMAN	TBC1 domain family, member 3G	495						plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			large_intestine(1)	1		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAGGGTGTTCAGCCTGCCAGCA	0.624																																																	0																																										SO:0001589	frameshift_variant	729877					17q12	2014-04-11			ENSG00000161583	ENSG00000260287			29860	protein-coding gene	gene with protein product						16863688	Standard			Approved			Q6DHY5	OTTHUMG00000132711	ENST00000330458.7:c.1485dupC	17.37:g.34746600_34746600dupG	ENSP00000332729:p.Ala495fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K8H9	Frame_Shift_Ins	INS	ENST00000330458.7	37																																																																																					0.624	TBC1D3G-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_001040282	
TEC	7006	hgsc.bcm.edu;ucsc.edu	37	4	48147535	48147535	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr4:48147535delA	ENST00000381501.3	-	13	1300	c.1143delT	c.(1141-1143)tttfs	p.F381fs	TEC_ENST00000511471.2_5'UTR	NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	381	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						TCACCACTCCAAACAGTCCAC	0.448																																																	0													146.0	130.0	135.0					4																	48147535		2203	4300	6503	SO:0001589	frameshift_variant	100124696			D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1143delT	4.37:g.48147535delA	ENSP00000370912:p.Phe381fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZKZ6|Q3MIS5	Frame_Shift_Del	DEL	ENST00000381501.3	37	CCDS3481.1																																																																																				0.448	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3			
THADA	63892	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	43801938	43801938	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr2:43801938G>C	ENST00000405006.4	-	11	1617	c.1266C>G	c.(1264-1266)caC>caG	p.H422Q	THADA_ENST00000404790.1_Missense_Mutation_p.H422Q|THADA_ENST00000415080.2_Missense_Mutation_p.H132Q|THADA_ENST00000330266.7_Missense_Mutation_p.H132Q|THADA_ENST00000405975.2_Missense_Mutation_p.H422Q|THADA_ENST00000403856.1_Missense_Mutation_p.H422Q|THADA_ENST00000402360.2_Missense_Mutation_p.H422Q	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	422								p.H422Q(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CAGTGAGCCGGTGCATTTGGA	0.418																																																	1	Substitution - Missense(1)	kidney(1)											154.0	146.0	149.0					2																	43801938		1890	4125	6015	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.1266C>G	2.37:g.43801938G>C	ENSP00000385995:p.His422Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.061636	0.55432	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.64618	1.43;1.43;1.43;1.43;-0.11;-0.11;1.43	5.84	1.96	0.26148	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73434	0.3586	M	0.68593	2.085	0.32332	N	0.560951	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.997	T	0.76979	-0.2758	10	0.87932	D	0	-4.718	9.5161	0.39106	0.4164:0.0:0.5836:0.0	.	422;422;422;132;422	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	Q	132;422;422;132;422;422;422;422	ENSP00000331105:H132Q;ENSP00000386088:H422Q;ENSP00000416048:H132Q;ENSP00000385995:H422Q;ENSP00000385441:H422Q;ENSP00000384266:H422Q;ENSP00000385469:H422Q	ENSP00000331105:H132Q	H	-	3	2	THADA	43655442	1.000000	0.71417	0.912000	0.35992	0.852000	0.48524	1.165000	0.31822	0.369000	0.24510	-0.221000	0.12465	CAC		0.418	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3		NM_022065	
TRIM21	6737	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	4411299	4411299	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr11:4411299C>T	ENST00000254436.7	-	2	453	c.341G>A	c.(340-342)tGt>tAt	p.C114Y	TRIM21_ENST00000543625.1_Missense_Mutation_p.C114Y	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	114					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C114Y(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		AGACTGGGCACATACCCAGCA	0.587																																																	1	Substitution - Missense(1)	kidney(1)											71.0	75.0	73.0					11																	4411299		2048	4196	6244	SO:0001583	missense	6737			AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	11312	protein-coding gene	gene with protein product		109092	"""Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)"", ""tripartite motif-containing 21"""	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.341G>A	11.37:g.4411299C>T	ENSP00000254436:p.Cys114Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5XPV5|Q96RF8	Missense_Mutation	SNP	ENST00000254436.7	37	CCDS44525.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696126	0.68386	.	.	ENSG00000132109	ENST00000254436;ENST00000543625	D;D	0.99080	-5.4;-5.4	4.32	4.32	0.51571	Zinc finger, B-box, chordata (1);Zinc finger, B-box (3);	0.000000	0.56097	D	0.000033	D	0.99560	0.9842	H	0.97874	4.095	0.38543	D	0.94927	D	0.89917	1.0	D	0.91635	0.999	D	0.97920	1.0314	10	0.87932	D	0	.	15.1289	0.72503	0.0:1.0:0.0:0.0	.	114	P19474	RO52_HUMAN	Y	114	ENSP00000254436:C114Y;ENSP00000444045:C114Y	ENSP00000254436:C114Y	C	-	2	0	TRIM21	4367875	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	5.177000	0.65032	2.691000	0.91804	0.561000	0.74099	TGT		0.587	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1		NM_003141	
Unknown	0	broad.mit.edu	37	12	92133	92133	+	IGR	SNP	G	G	T	rs374355671		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr12:92133G>T								AC215219.1 (18811 upstream) : AC026369.1 (54918 downstream)																							GCAGCTGCCTGTCAGGAAGAG	0.592																																																	0																																										SO:0001628	intergenic_variant	0																															12.37:g.92133G>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.592									
USP36	57602	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	76795062	76795062	+	Silent	SNP	A	A	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr17:76795062A>C	ENST00000542802.3	-	19	3611	c.3168T>G	c.(3166-3168)gcT>gcG	p.A1056A	USP36_ENST00000312010.6_Silent_p.A1056A|USP36_ENST00000449938.2_Silent_p.A661A			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	1054					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.A1056A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			TGTCTTCAATAGCATCCTGAC	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											260.0	210.0	227.0					17																	76795062		2203	4300	6503	SO:0001819	synonymous_variant	57602			AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.3168T>G	17.37:g.76795062A>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																				0.577	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3		NM_025090	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10191540	10191540	+	Frame_Shift_Del	DEL	T	T	-	rs5030822		TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr3:10191540delT	ENST00000256474.2	+	3	1373	c.533delT	c.(532-534)ctgfs	p.L178fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Frame_Shift_Del_p.L137fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	178			L -> P (in VHLD; type I-II; common mutation). {ECO:0000269|PubMed:8956040}.|L -> Q (in VHLD; type II; dbSNP:rs5030822).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L178R(1)|p.R177fs*37(1)|p.L178_V181del(1)|p.?fs(1)|p.Y175_L178>*(1)|p.L178fs*36(1)|p.D179fs*36(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACAGGAGACTGGACATCGTC	0.527		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	7	Insertion - Frameshift(2)|Deletion - In frame(1)|Deletion - Frameshift(1)|Complex - frameshift(1)|Complex - deletion inframe(1)|Substitution - Missense(1)	kidney(7)	GRCh37	CM003061|CM941386|CM961439	VHL	M	rs5030822						89.0	80.0	83.0					3																	10191540		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.533delT	3.37:g.10191540delT	ENSP00000256474:p.Leu178fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.527	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VWF	7450	hgsc.bcm.edu	37	12	6127651	6127652	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr12:6127651_6127652insC	ENST00000261405.5	-	28	5186_5187	c.4932_4933insG	c.(4930-4935)tggcccfs	p.P1645fs		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1645	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GGGGCATTGGGCCAGCCAATCC	0.619																																																	0																																										SO:0001589	frameshift_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4933dupG	12.37:g.6127653_6127653dupC	ENSP00000261405:p.Pro1645fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TCE8|Q99806	Frame_Shift_Ins	INS	ENST00000261405.5	37	CCDS8539.1																																																																																				0.619	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1		NM_000552	
ZFHX3	463	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	72829790	72829790	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3349-01A-01D-1251-10	TCGA-A3-3349-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b257f6-9cb5-4598-89c7-f0b55e24dbb3	aa4a92b2-92ab-48d5-a8e5-9e84319e1799	g.chr16:72829790T>G	ENST00000268489.5	-	9	7463	c.6791A>C	c.(6790-6792)aAt>aCt	p.N2264T	ZFHX3_ENST00000397992.5_Missense_Mutation_p.N1350T	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2264					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.N2264T(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGGGTAAGCATTGGCATCGAA	0.488																																																	1	Substitution - Missense(1)	kidney(1)											209.0	198.0	202.0					16																	72829790		2198	4300	6498	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6791A>C	16.37:g.72829790T>G	ENSP00000268489:p.Asn2264Thr	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046946	0.55110	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	D;D	0.96168	-3.93;-3.93	5.79	5.79	0.91817	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.53938	D	0.000059	D	0.94837	0.8332	N	0.16307	0.4	0.80722	D	1	D	0.61080	0.989	P	0.62560	0.904	D	0.96042	0.9025	10	0.72032	D	0.01	.	16.1193	0.81336	0.0:0.0:0.0:1.0	.	2264	Q15911	ZFHX3_HUMAN	T	2264;1350	ENSP00000268489:N2264T;ENSP00000438926:N1350T	ENSP00000268489:N2264T	N	-	2	0	ZFHX3	71387291	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	AAT		0.488	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1		NM_006885	
