#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CROCCP2	84809	broad.mit.edu	37	1	16957420	16957420	+	lincRNA	SNP	G	G	C	rs11589767	byFrequency	TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr1:16957420G>C	ENST00000412962.1	-	0	258							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											AGGGCGGAGAGAATCAGGGCA	0.701													.|||	50	0.00998403	0.0333	0.0029	5008	,	,		37828	0.0		0.001	False		,,,				2504	0.0031					ENST00000412962.1																			0																																																			0							g.chr1:16957420G>C	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.16957420G>C														0	258	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.701	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		5	16	0	0	0	0.003080	0	5	16				
MAN2C1	4123	broad.mit.edu	37	15	75660529	75660529	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr15:75660529C>T	ENST00000267978.5	-	2	158	c.112G>A	c.(112-114)Gcc>Acc	p.A38T	MAN2C1_ENST00000565683.1_Missense_Mutation_p.A38T|MAN2C1_ENST00000563539.1_5'UTR|MAN2C1_ENST00000563622.1_Missense_Mutation_p.A38T|RP11-817O13.8_ENST00000563278.1_lincRNA|MAN2C1_ENST00000569482.1_Missense_Mutation_p.A38T	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	38					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						GGGCAGCTGGCCCCAAAAAGC	0.711																																						ENST00000565683.1																			0				central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						c.(112-114)Gcc>Acc		mannosidase, alpha, class 2C, member 1							8.0	10.0	10.0					15																	75660529		2105	4152	6257	SO:0001583	missense	4123				mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding	g.chr15:75660529C>T	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.112G>A	15.37:g.75660529C>T	ENSP00000267978:p.Ala38Thr					MAN2C1_ENST00000267978.5_Missense_Mutation_p.A38T|MAN2C1_ENST00000569482.1_Missense_Mutation_p.A38T|MAN2C1_ENST00000563539.1_5'UTR|RP11-817O13.8_ENST00000563278.1_lincRNA|MAN2C1_ENST00000563622.1_Missense_Mutation_p.A38T	p.A38T	NM_001256494.1	NP_001243423.1	Q9NTJ4	MA2C1_HUMAN			2	123	-			38					H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	37	c.112G>A	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	C	9.229	1.035264	0.19590	.	.	ENSG00000140400	ENST00000267978;ENST00000421803	T	0.18174	2.23	5.1	3.14	0.36123	.	0.410909	0.24988	N	0.034014	T	0.11281	0.0275	L	0.31578	0.945	0.24941	N	0.991855	B;B;B	0.21753	0.06;0.06;0.06	B;B;B	0.22601	0.04;0.018;0.018	T	0.34079	-0.9843	10	0.14252	T	0.57	-5.3625	9.7064	0.40218	0.1596:0.6865:0.1539:0.0	.	38;38;38	B4DH23;Q68EM8;Q9NTJ4	.;.;MA2C1_HUMAN	T	38	ENSP00000267978:A38T	ENSP00000267978:A38T	A	-	1	0	MAN2C1	73447582	1.000000	0.71417	0.967000	0.41034	0.106000	0.19336	4.863000	0.62983	0.492000	0.27815	0.484000	0.47621	GCC		0.711	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			5	8	0	0	0	0.000602	0	5	8				
FRG1B	284802	broad.mit.edu	37	20	29628236	29628236	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr20:29628236G>C	ENST00000278882.3	+	6	618	c.238G>C	c.(238-240)Gct>Cct	p.A80P	FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	80								p.A80P(8)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGGAAAATGGCTTTGTTGGC	0.363																																						ENST00000278882.3																			8	Substitution - Missense(8)	p.A80P(8)	prostate(4)|kidney(4)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(238-240)Gct>Cct																																						SO:0001583	missense	0							g.chr20:29628236G>C			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.238G>C	20.37:g.29628236G>C	ENSP00000278882:p.Ala80Pro					FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P	p.A80P							6	618	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.238G>C		.	.	.	.	.	.	.	.	.	.	g	15.73	2.920277	0.52653	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.57595	0.39	2.08	2.08	0.27032	Actin cross-linking (1);	0.052409	0.85682	D	0.000000	T	0.68952	0.3057	.	.	.	0.80722	D	1	D;D	0.64830	0.994;0.988	D;D	0.85130	0.997;0.993	T	0.72766	-0.4194	9	0.87932	D	0	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	85;80	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	P	80;85;80	ENSP00000408863:A85P	ENSP00000278882:A80P	A	+	1	0	FRG1B	28241897	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	8.494000	0.90477	1.475000	0.48197	0.423000	0.28283	GCT		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	69	0	0	0	0.001168	0	5	69				
NBEAL2	23218	broad.mit.edu	37	3	47030166	47030166	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr3:47030166T>C	ENST00000450053.3	+	2	238	c.59T>C	c.(58-60)cTg>cCg	p.L20P	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.L20P	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	20					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CAGAAGGACCTGGGTTACCTG	0.562																																						ENST00000450053.3																			0				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						c.(58-60)cTg>cCg		neurobeachin-like 2							101.0	102.0	101.0					3																	47030166		2043	4177	6220	SO:0001583	missense	23218						binding	g.chr3:47030166T>C	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.59T>C	3.37:g.47030166T>C	ENSP00000415034:p.Leu20Pro					NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.L20P	p.L20P	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)	2	238	+		Acute lymphoblastic leukemia(5;0.0534)	20					O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	c.59T>C	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.491347	0.44249	.	.	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.56275	0.47;0.48	4.17	3.01	0.34805	.	.	.	.	.	T	0.50956	0.1646	N	0.20685	0.6	0.80722	D	1	D;P	0.89917	1.0;0.895	D;P	0.74674	0.984;0.467	T	0.47774	-0.9091	9	0.44086	T	0.13	.	5.6593	0.17660	0.0:0.2162:0.0:0.7838	.	13;20	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	P	20;20;13	ENSP00000292309:L20P;ENSP00000415034:L20P	ENSP00000292309:L20P	L	+	2	0	NBEAL2	47005170	1.000000	0.71417	0.995000	0.50966	0.874000	0.50279	3.894000	0.56250	0.661000	0.30985	0.459000	0.35465	CTG		0.562	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		3	110	0	0	0	0.004672	0	3	110				
WASH2P	375260	broad.mit.edu	37	2	114355098	114355098	+	RNA	SNP	G	G	A			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr2:114355098G>A	ENST00000538033.2	+	0	2037							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CGACCCCTCCGGTGGCCGGGC	0.647																																						ENST00000538033.2																			0																																																			0							g.chr2:114355098G>A			2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114355098G>A														0	2037	+									RNA	SNP	ENST00000538033.2	37																																																																																						0.647	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1	NM_198943		8	18	0	0	0	0.004482	0	8	18				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		15	20	0	0	0	0.002450	0	15	20				
FRG1B	284802	broad.mit.edu	37	20	29628310	29628310	+	Silent	SNP	A	A	G	rs111939959		TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr20:29628310A>G	ENST00000278882.3	+	6	692	c.312A>G	c.(310-312)gcA>gcG	p.A104A	FRG1B_ENST00000358464.4_Silent_p.A104A|FRG1B_ENST00000439954.2_Silent_p.A109A			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	104										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTAAAACAGCAGGAGAAGAAG	0.358																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(310-312)gcA>gcG																																						SO:0001819	synonymous_variant	0							g.chr20:29628310A>G			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.312A>G	20.37:g.29628310A>G						FRG1B_ENST00000358464.4_Silent_p.A104A|FRG1B_ENST00000439954.2_Silent_p.A109A	p.A104A							6	692	+								C4AME5	Silent	SNP	ENST00000278882.3	37	c.312A>G																																																																																					0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		3	32	0	0	0	0.004672	0	3	32				
LRRC37A2	474170	broad.mit.edu	37	17	44626432	44626432	+	Missense_Mutation	SNP	A	A	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr17:44626432A>C	ENST00000576629.1	+	10	4422	c.3927A>C	c.(3925-3927)aaA>aaC	p.K1309N	LRRC37A2_ENST00000333412.3_Missense_Mutation_p.K1309N|ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000445552.2_Intron|ARL17A_ENST00000337845.7_Intron|ARL17A_ENST00000573185.1_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1309						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GCTTTCACAAAACTCGCTCCC	0.428																																						ENST00000576629.1																			0				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15						c.(3925-3927)aaA>aaC		leucine rich repeat containing 37, member A2							143.0	243.0	209.0					17																	44626432		2184	4296	6480	SO:0001583	missense	474170					integral to membrane		g.chr17:44626432A>C	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.3927A>C	17.37:g.44626432A>C	ENSP00000459551:p.Lys1309Asn					ARL17A_ENST00000445552.2_Intron|ARL17A_ENST00000573185.1_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.K1309N|ARL17A_ENST00000337845.7_Intron|ARL17A_ENST00000329240.4_Intron	p.K1309N			A6NM11	L37A2_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.232)	10	4422	+		Melanoma(429;0.211)	1309					B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	c.3927A>C	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	a	11.77	1.736711	0.30774	.	.	ENSG00000238083	ENST00000333412	T	0.60920	0.15	2.35	1.25	0.21368	.	.	.	.	.	T	0.60314	0.2259	L	0.40543	1.245	0.09310	N	1	D;P;P	0.57899	0.981;0.865;0.779	D;P;B	0.67231	0.95;0.615;0.311	T	0.46721	-0.9171	9	0.72032	D	0.01	.	3.6001	0.08021	0.7951:0.0:0.2049:0.0	.	1309;270;1309	C9JSP5;B3KRJ4;A6NM11	.;.;L37A2_HUMAN	N	1309	ENSP00000333071:K1309N	ENSP00000333071:K1309N	K	+	3	2	LRRC37A2	41981748	0.000000	0.05858	0.015000	0.15790	0.017000	0.09413	0.488000	0.22371	1.090000	0.41315	0.147000	0.16070	AAA		0.428	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607		68	243	0	0	0	0.003610	0	68	243				
SEC24D	9871	broad.mit.edu	37	4	119754779	119754779	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr4:119754779G>A	ENST00000280551.6	-	2	311	c.73C>T	c.(73-75)Cat>Tat	p.H25Y	SEC24D_ENST00000419654.2_5'UTR|SEC24D_ENST00000379735.5_Missense_Mutation_p.H25Y			O94855	SC24D_HUMAN	SEC24 family member D	25	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						TGCCCATAATGAGGTGGAGAA	0.443																																						ENST00000379735.5																			0				breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						c.(73-75)Cat>Tat		SEC24 family member D							165.0	151.0	156.0					4																	119754779		2203	4300	6503	SO:0001583	missense	9871				COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding	g.chr4:119754779G>A	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.73C>T	4.37:g.119754779G>A	ENSP00000280551:p.His25Tyr					SEC24D_ENST00000280551.6_Missense_Mutation_p.H25Y|SEC24D_ENST00000419654.2_5'UTR	p.H25Y	NM_014822.2	NP_055637.2	O94855	SC24D_HUMAN			2	344	-			25			Pro-rich.		Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	37	c.73C>T	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.096897	0.37048	.	.	ENSG00000150961	ENST00000280551;ENST00000379735;ENST00000503683	T;T;T	0.75938	-0.97;-0.98;0.82	6.02	4.29	0.51040	.	0.284754	0.40302	N	0.001122	T	0.58409	0.2120	L	0.27053	0.805	0.80722	D	1	B;B	0.22909	0.077;0.046	B;B	0.28011	0.085;0.039	T	0.50136	-0.8863	10	0.02654	T	1	-20.0949	12.0758	0.53643	0.0:0.0:0.6862:0.3138	.	25;25	O94855-2;O94855	.;SC24D_HUMAN	Y	25	ENSP00000280551:H25Y;ENSP00000369059:H25Y;ENSP00000426309:H25Y	ENSP00000280551:H25Y	H	-	1	0	SEC24D	119974227	0.999000	0.42202	0.607000	0.28956	0.914000	0.54420	2.845000	0.48254	0.856000	0.35383	0.650000	0.86243	CAT		0.443	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			41	64	0	0	0	0.002222	0	41	64				
OCLN	100506658	broad.mit.edu	37	5	68805542	68805542	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr5:68805542G>A	ENST00000355237.2	+	3	1061	c.625G>A	c.(625-627)Ggt>Agt	p.G209S	OCLN_ENST00000380766.2_Missense_Mutation_p.G209S|OCLN_ENST00000542132.1_Intron|OCLN_ENST00000538151.1_Intron|OCLN_ENST00000396442.2_Missense_Mutation_p.G209S	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	209	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		ATCTCTATATGGTTCACAAAT	0.423																																						ENST00000355237.2																			0				endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6						c.(625-627)Ggt>Agt		occludin							198.0	196.0	197.0					5																	68805542		2203	4300	6503	SO:0001583	missense	100506658				cellular component disassembly involved in apoptosis|protein complex assembly	integral to membrane|tight junction	protein binding|structural molecule activity	g.chr5:68805542G>A	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"""tight junction protein occludin TM4 minus"", ""phosphatase 1, regulatory subunit 115"""	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.625G>A	5.37:g.68805542G>A	ENSP00000347379:p.Gly209Ser					OCLN_ENST00000380766.2_Missense_Mutation_p.G209S|OCLN_ENST00000542132.1_Intron|OCLN_ENST00000538151.1_Intron|OCLN_ENST00000396442.2_Missense_Mutation_p.G209S	p.G209S	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)	3	1061	+		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)	209			MARVEL.		B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	37	c.625G>A	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	G	6.806	0.517859	0.13005	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766	T;T;D	0.83591	0.38;0.38;-1.74	5.81	-5.24	0.02789	Marvel (1);MARVEL-like domain (1);	0.662498	0.17321	N	0.178506	T	0.57036	0.2026	N	0.05574	-0.02	0.42351	D	0.992377	B	0.09022	0.002	B	0.11329	0.006	T	0.32561	-0.9902	10	0.11182	T	0.66	-40.9608	8.5879	0.33668	0.2281:0.0:0.5977:0.1742	.	209	Q16625	OCLN_HUMAN	S	209	ENSP00000347379:G209S;ENSP00000379719:G209S;ENSP00000370143:G209S	ENSP00000347379:G209S	G	+	1	0	OCLN	68841298	0.001000	0.12720	0.131000	0.22000	0.759000	0.43091	0.073000	0.14640	-0.630000	0.05567	0.650000	0.86243	GGT		0.423	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538		76	97	0	0	0	0.003610	0	76	97				
NOLC1	9221	broad.mit.edu	37	10	103921613	103921613	+	Silent	SNP	A	A	T			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr10:103921613A>T	ENST00000605788.1	+	12	2107	c.1872A>T	c.(1870-1872)ccA>ccT	p.P624P	NOLC1_ENST00000477977.1_3'UTR|NOLC1_ENST00000405356.1_Silent_p.P634P|NOLC1_ENST00000488254.2_Silent_p.P625P|NOLC1_ENST00000603742.1_Silent_p.P343P	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	624					cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		CATCATCCCCATTCCGAAGGG	0.473																																						ENST00000405356.1																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31						c.(1900-1902)ccA>ccT		nucleolar and coiled-body phosphoprotein 1							71.0	68.0	69.0					10																	103921613		2203	4300	6503	SO:0001819	synonymous_variant	9221				mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding	g.chr10:103921613A>T	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1872A>T	10.37:g.103921613A>T						NOLC1_ENST00000605788.1_Silent_p.P624P|NOLC1_ENST00000477977.1_3'UTR|NOLC1_ENST00000488254.2_Silent_p.P625P|NOLC1_ENST00000603742.1_Silent_p.P343P	p.P634P			Q14978	NOLC1_HUMAN		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)	12	2137	+		Colorectal(252;0.122)	624					Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	c.1902A>T	CCDS7530.1																																																																																				0.473	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		24	40	0	0	0	0.003330	0	24	40				
MAS1L	116511	broad.mit.edu	37	6	29454710	29454710	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr6:29454710T>C	ENST00000377127.3	-	1	1028	c.970A>G	c.(970-972)Agg>Ggg	p.R324G		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	324					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R324G(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						TCCTTCAGCCTTTTCTTTCTG	0.463																																					NSCLC(153;755 1987 3859 11251 32945)	ENST00000377127.3																			1	Substitution - Missense(1)	p.R324G(1)	prostate(1)	NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						c.(970-972)Agg>Ggg		MAS1 oncogene-like							94.0	100.0	98.0					6																	29454710		2203	4300	6503	SO:0001583	missense	116511					cytoplasm|integral to membrane|nucleus|plasma membrane	G-protein coupled receptor activity	g.chr6:29454710T>C	S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"""GPCR / Class A : Orphans"""	13961	protein-coding gene	gene with protein product		607235	"""MAS1 oncogene-like"""				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.970A>G	6.37:g.29454710T>C	ENSP00000366331:p.Arg324Gly						p.R324G	NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN			1	1028	-			324					Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	c.970A>G	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	T	7.400	0.632554	0.14322	.	.	ENSG00000204687	ENST00000377127	T	0.37584	1.19	2.36	-0.36	0.12568	.	.	.	.	.	T	0.14527	0.0351	L	0.39633	1.23	0.09310	N	1	B	0.29378	0.243	B	0.36845	0.234	T	0.38134	-0.9675	9	0.56958	D	0.05	.	8.1955	0.31394	0.0:0.0:0.4246:0.5754	.	324	P35410	MAS1L_HUMAN	G	324	ENSP00000366331:R324G	ENSP00000366331:R324G	R	-	1	2	MAS1L	29562689	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.995000	0.03712	-0.236000	0.09753	-0.612000	0.04053	AGG		0.463	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		3	126	0	0	0	0.004672	0	3	126				
LRIT1	26103	broad.mit.edu	37	10	85997395	85997395	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr10:85997395A>G	ENST00000372105.3	-	2	191	c.170T>C	c.(169-171)aTc>aCc	p.I57T		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	57	LRRNT.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						GTCCGGGGGGATGGACGCCGG	0.667																																						ENST00000372105.3																			0				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						c.(169-171)aTc>aCc		leucine-rich repeat, immunoglobulin-like and transmembrane domains 1							35.0	40.0	38.0					10																	85997395		2152	4185	6337	SO:0001583	missense	26103					integral to endoplasmic reticulum membrane		g.chr10:85997395A>G	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.170T>C	10.37:g.85997395A>G	ENSP00000361177:p.Ile57Thr						p.I57T	NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN			2	191	-			57			LRRNT.		Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	c.170T>C	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660654	0.47572	.	.	ENSG00000148602	ENST00000372105	T	0.40756	1.02	5.46	5.46	0.80206	Leucine-rich repeat-containing N-terminal (1);	0.434743	0.24443	N	0.038481	T	0.43897	0.1268	M	0.63843	1.955	0.44956	D	0.99797	B	0.33549	0.417	B	0.35182	0.197	T	0.47995	-0.9073	10	0.87932	D	0	.	13.0556	0.58977	1.0:0.0:0.0:0.0	.	57	Q9P2V4	LRIT1_HUMAN	T	57	ENSP00000361177:I57T	ENSP00000361177:I57T	I	-	2	0	LRIT1	85987375	1.000000	0.71417	0.147000	0.22382	0.487000	0.33371	8.888000	0.92464	2.079000	0.62486	0.533000	0.62120	ATC		0.667	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		3	72	0	0	0	0.000248	0	3	72				
NINJ2	4815	broad.mit.edu	37	12	772557	772557	+	Silent	SNP	C	C	A			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr12:772557C>A	ENST00000305108.4	-	1	388	c.108G>T	c.(106-108)ccG>ccT	p.P36P	RP11-218M22.1_ENST00000543884.1_RNA	NM_016533.4	NP_057617.2	Q9NZG7	NINJ2_HUMAN	ninjurin 2	0					nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|tissue regeneration (GO:0042246)	integral component of plasma membrane (GO:0005887)				large_intestine(3)|lung(1)|ovary(2)	6	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			TCACACGCACCGGGTGCCGGG	0.597																																						ENST00000305108.4																			0				large_intestine(3)|lung(1)|ovary(2)	6						c.(106-108)ccG>ccT		ninjurin 2							111.0	116.0	114.0					12																	772557		2203	4300	6503	SO:0001819	synonymous_variant	4815				nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane		g.chr12:772557C>A	AF205633	CCDS8505.1, CCDS73418.1	12p13	2008-08-05			ENSG00000171840	ENSG00000171840			7825	protein-coding gene	gene with protein product		607297				10627596	Standard	XM_005253689		Approved		uc001qil.3	Q9NZG7	OTTHUMG00000090311	ENST00000305108.4:c.108G>T	12.37:g.772557C>A						RP11-218M22.1_ENST00000543884.1_RNA	p.P36P	NM_016533.4	NP_057617.2	Q9NZG7	NINJ2_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)		1	388	-	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		0						Silent	SNP	ENST00000305108.4	37	c.108G>T	CCDS8505.1																																																																																				0.597	NINJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206673.2	NM_016533		5	194	1	0	0.00116845	0.001168	0.00878671	5	194				
SPAG17	200162	broad.mit.edu	37	1	118644485	118644485	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr1:118644485T>C	ENST00000336338.5	-	5	577	c.512A>G	c.(511-513)aAg>aGg	p.K171R		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	171	Lys-rich.					cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACTTGGAGCCTTTTTCTCCTT	0.438																																						ENST00000336338.5																			0				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123						c.(511-513)aAg>aGg		sperm associated antigen 17							207.0	191.0	196.0					1																	118644485		2203	4300	6503	SO:0001583	missense	200162					cilium|flagellar axoneme|microtubule		g.chr1:118644485T>C		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.512A>G	1.37:g.118644485T>C	ENSP00000337804:p.Lys171Arg						p.K171R	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN		Lung(183;0.0858)	5	577	-	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)	171			Lys-rich.		Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	c.512A>G	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.403108	0.25291	.	.	ENSG00000155761	ENST00000336338	T	0.23754	1.89	5.39	4.18	0.49190	.	0.546163	0.18560	N	0.137643	T	0.25344	0.0616	L	0.42581	1.335	0.22500	N	0.999045	D	0.71674	0.998	D	0.66196	0.942	T	0.02698	-1.1122	10	0.56958	D	0.05	.	10.0216	0.42046	0.0:0.0:0.1691:0.8309	.	171	Q6Q759	SPG17_HUMAN	R	171	ENSP00000337804:K171R	ENSP00000337804:K171R	K	-	2	0	SPAG17	118446008	0.987000	0.35691	0.943000	0.38184	0.017000	0.09413	1.338000	0.33873	2.168000	0.68352	0.533000	0.62120	AAG		0.438	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		3	114	0	0	0	0.004672	0	3	114				
TOP2A	7153	broad.mit.edu	37	17	38552660	38552660	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr17:38552660T>C	ENST00000423485.1	-	28	3753	c.3595A>G	c.(3595-3597)Aag>Gag	p.K1199E		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1199					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCCTTGGCCTTCCCCCCTTTC	0.428																																						ENST00000423485.1																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39						c.(3595-3597)Aag>Gag		topoisomerase (DNA) II alpha 170kDa	Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)						117.0	109.0	111.0					17																	38552660		1842	4089	5931	SO:0001583	missense	7153				apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding	g.chr17:38552660T>C		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3595A>G	17.37:g.38552660T>C	ENSP00000411532:p.Lys1199Glu						p.K1199E	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	STAD - Stomach adenocarcinoma(5;0.00183)		28	3753	-		Breast(137;0.00328)	1199					B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	c.3595A>G	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.325015	0.60634	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.25749	1.78	5.93	5.93	0.95920	.	0.211585	0.49305	D	0.000144	T	0.29256	0.0728	M	0.67397	2.05	0.80722	D	1	P	0.36789	0.57	B	0.31946	0.138	T	0.05131	-1.0904	10	0.42905	T	0.14	.	16.3766	0.83401	0.0:0.0:0.0:1.0	.	1199	P11388	TOP2A_HUMAN	E	1199;1279;1222;1235	ENSP00000411532:K1199E	ENSP00000269577:K1279E	K	-	1	0	TOP2A	35806186	1.000000	0.71417	0.968000	0.41197	0.332000	0.28634	7.386000	0.79775	2.263000	0.75096	0.533000	0.62120	AAG		0.428	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			3	107	0	0	0	0.004672	0	3	107				
PKHD1	5314	broad.mit.edu	37	6	51900420	51900420	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr6:51900420G>A	ENST00000371117.3	-	28	3472	c.3197C>T	c.(3196-3198)tCa>tTa	p.S1066L	PKHD1_ENST00000340994.4_Missense_Mutation_p.S1066L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1066	IPT/TIG 5.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AATTCTGCTTGAATTGCTTGT	0.453																																						ENST00000371117.3																			0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304						c.(3196-3198)tCa>tTa		polycystic kidney and hepatic disease 1 (autosomal recessive)							147.0	133.0	138.0					6																	51900420		2203	4300	6503	SO:0001583	missense	5314				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	g.chr6:51900420G>A	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3197C>T	6.37:g.51900420G>A	ENSP00000360158:p.Ser1066Leu					PKHD1_ENST00000340994.4_Missense_Mutation_p.S1066L	p.S1066L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN			28	3472	-	Lung NSC(77;0.0605)		1066			IPT/TIG 5.		Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	c.3197C>T	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	9.636	1.137580	0.21123	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80653	-1.4;-1.4	5.69	4.63	0.57726	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.372474	0.23165	N	0.051193	T	0.64918	0.2642	M	0.62723	1.935	0.09310	N	1	P;P	0.44429	0.802;0.835	B;B	0.40864	0.231;0.342	T	0.62798	-0.6778	10	0.11182	T	0.66	.	14.6306	0.68653	0.0821:0.0:0.9179:0.0	.	1066;1066	P08F94-2;P08F94	.;PKHD1_HUMAN	L	1066	ENSP00000360158:S1066L;ENSP00000341097:S1066L	ENSP00000341097:S1066L	S	-	2	0	PKHD1	52008379	1.000000	0.71417	0.545000	0.28153	0.283000	0.27025	4.821000	0.62679	2.690000	0.91761	0.650000	0.86243	TCA		0.453	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		43	47	0	0	0	0.003214	0	43	47				
CACNA2D1	781	broad.mit.edu	37	7	81695842	81695843	+	Splice_Site	INS	-	-	A	rs370103843		TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr7:81695842_81695843insA	ENST00000356253.5	-	8	914		c.e8-2		CACNA2D1_ENST00000423588.1_Splice_Site|CACNA2D1_ENST00000356860.3_Splice_Site			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1						calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	ATGGTGAAGCTAAAAAAAAAAA	0.272																																						ENST00000356860.3																			0				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81						c.e8-2		calcium channel, voltage-dependent, alpha 2/delta subunit 1	Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)																																			SO:0001630	splice_region_variant	781					voltage-gated calcium channel complex	metal ion binding	g.chr7:81695842_81695843insA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.659-2->T	7.37:g.81695853_81695853dupA						CACNA2D1_ENST00000356253.5_Splice_Site|CACNA2D1_ENST00000423588.1_Splice_Site		NM_000722.2	NP_000713.2	P54289	CA2D1_HUMAN			8	997	-								Q17R45|Q9UD80|Q9UD81|Q9UD82	Splice_Site	INS	ENST00000356253.5	37																																																																																						0.272	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			Intron	8	24						8	24	---	---	---	---
RP13-329D4.3	0	broad.mit.edu	37	20	26113543	26113543	+	lincRNA	DEL	A	A	-	rs375245697		TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr20:26113543delA	ENST00000416563.1	-	0	250																											TCTTTGCCTTAACAACATTAT	0.363																																						ENST00000416563.1																			0																																																			0							g.chr20:26113543delA																													20.37:g.26113543delA														0	250	-									RNA	DEL	ENST00000416563.1	37																																																																																						0.363	RP13-329D4.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000078482.1			3	4						3	4	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085940	11085942	+	RNA	DEL	CAC	CAC	-			TCGA-ET-A25O-01A-11D-A17V-08	TCGA-ET-A25O-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c5a02689-c17c-4178-bdc1-20962476fefe	931159d9-99d5-4c5b-9200-8b6aac91918f	g.chr21:11085940_11085942delCAC	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccaccaccatcaccaccaccacc	0.532																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085940_11085942delCAC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11085949_11085951delCAC												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																						0.532	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		3	3						3	3	---	---	---	---
