#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
SIN3A	25942	broad.mit.edu	37	15	75688839	75688839	+	Splice_Site	SNP	T	T	C			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr15:75688839T>C	ENST00000394947.3	-	13	2169		c.e13-2		SIN3A_ENST00000394949.4_Splice_Site|SIN3A_ENST00000360439.4_Splice_Site	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						TACATCAAGCTGAAGAGGAAG	0.413																																						ENST00000394947.3																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						c.e13-2		SIN3 transcription regulator family member A							57.0	57.0	57.0					15																	75688839		2197	4294	6491	SO:0001630	splice_region_variant	25942				blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding	g.chr15:75688839T>C	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"""SIN3 homolog A, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog A (yeast)"""			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1855-2A>G	15.37:g.75688839T>C						SIN3A_ENST00000394949.4_Splice_Site|SIN3A_ENST00000360439.4_Splice_Site		NM_001145358.1	NP_001138830.1	Q96ST3	SIN3A_HUMAN			13	2169	-									Splice_Site	SNP	ENST00000394947.3	37		CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.663488	0.88251	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8218	0.78654	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SIN3A	73475892	1.000000	0.71417	0.979000	0.43373	0.958000	0.62258	7.999000	0.88496	2.326000	0.78906	0.533000	0.62120	.		0.413	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	Intron	5	42	0	0	0	1	0	5	42				
SLC1A2	6506	broad.mit.edu	37	11	35336644	35336644	+	Missense_Mutation	SNP	G	G	C	rs377633002		TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr11:35336644G>C	ENST00000278379.3	-	3	518	c.236C>G	c.(235-237)gCc>gGc	p.A79G	SLC1A2_ENST00000395750.1_Missense_Mutation_p.A70G|SLC1A2_ENST00000606205.1_Missense_Mutation_p.A79G|SLC1A2_ENST00000395753.1_Missense_Mutation_p.A70G	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	79					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			CCCTGGGAAGGCTATTAACAT	0.478																																					NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	ENST00000278379.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24						c.(235-237)gCc>gGc		solute carrier family 1 (glial high affinity glutamate transporter), member 2	L-Glutamic Acid(DB00142)	G	GLY/ALA,GLY/ALA	0,4404		0,0,2202	119.0	112.0	114.0		236,209	5.7	1.0	11		114	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense	SLC1A2	NM_004171.3,NM_001195728.1	60,60	0,1,6499	CC,CG,GG		0.0116,0.0,0.0077	benign,benign	79/575,70/566	35336644	1,12999	2202	4298	6500	SO:0001583	missense	6506				D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity	g.chr11:35336644G>C	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.236C>G	11.37:g.35336644G>C	ENSP00000278379:p.Ala79Gly					SLC1A2_ENST00000395753.1_Missense_Mutation_p.A70G|SLC1A2_ENST00000606205.1_Missense_Mutation_p.A79G|SLC1A2_ENST00000395750.1_Missense_Mutation_p.A70G	p.A79G	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	STAD - Stomach adenocarcinoma(6;0.00731)		3	518	-	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	79					B4DQE9|Q14417|Q541G6|U3KQQ4	Missense_Mutation	SNP	ENST00000278379.3	37	c.236C>G	CCDS31459.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200428	0.58126	0.0	1.16E-4	ENSG00000110436	ENST00000278379;ENST00000395750;ENST00000395753;ENST00000449068	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	5.66	5.66	0.87406	.	0.090866	0.85682	D	0.000000	T	0.39937	0.1097	N	0.05158	-0.105	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.006	T	0.19712	-1.0297	10	0.23302	T	0.38	-16.4722	19.7318	0.96183	0.0:0.0:1.0:0.0	.	79;79	B4DQE9;P43004	.;EAA2_HUMAN	G	79;70;70;75	ENSP00000278379:A79G;ENSP00000379099:A70G;ENSP00000379102:A70G;ENSP00000406133:A75G	ENSP00000278379:A79G	A	-	2	0	SLC1A2	35293220	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	9.822000	0.99363	2.674000	0.91012	0.561000	0.74099	GCC		0.478	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		5	56	0	0	0	1	0	5	56				
CLCNKB	1188	broad.mit.edu	37	1	16377498	16377498	+	Silent	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr1:16377498G>A	ENST00000375679.4	+	12	1293	c.1182G>A	c.(1180-1182)ccG>ccA	p.P394P	CLCNKB_ENST00000375667.3_Silent_p.P225P	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	394					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		GGTACCACCCGCGGTTCACCA	0.632																																						ENST00000375679.4																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21						c.(1180-1182)ccG>ccA		chloride channel, voltage-sensitive Kb							91.0	96.0	94.0					1																	16377498		2203	4300	6503	SO:0001819	synonymous_variant	1188							g.chr1:16377498G>A	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1182G>A	1.37:g.16377498G>A						CLCNKB_ENST00000375667.3_Silent_p.P225P	p.P394P	NM_000085.4	NP_000076.2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	12	1293	+		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)						B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	c.1182G>A	CCDS168.1																																																																																				0.632	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		10	49	0	0	0	1	0	10	49				
MAST3	23031	broad.mit.edu	37	19	18248097	18248097	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr19:18248097G>A	ENST00000262811.6	+	18	1934	c.1934G>A	c.(1933-1935)tGg>tAg	p.W645*		NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	645	AGC-kinase C-terminal.						ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GCCCTGGACTGGGCAGGGCTT	0.622																																						ENST00000262811.5																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						c.(1933-1935)tGg>tAg		microtubule associated serine/threonine kinase 3							62.0	69.0	67.0					19																	18248097		2037	4178	6215	SO:0001587	stop_gained	23031						ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	g.chr19:18248097G>A	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.1934G>A	19.37:g.18248097G>A	ENSP00000262811:p.Trp645*						p.W645*	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN			18	1934	+			645			AGC-kinase C-terminal.		Q7LDZ8|Q9UPI0	Nonsense_Mutation	SNP	ENST00000262811.6	37	c.1934G>A	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	G	39	7.428624	0.98279	.	.	ENSG00000099308	ENST00000262811	.	.	.	4.17	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6613	15.4848	0.75557	0.0:0.0:1.0:0.0	.	.	.	.	X	645	.	ENSP00000262811:W645X	W	+	2	0	MAST3	18109097	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.798000	0.99111	1.897000	0.54924	0.491000	0.48974	TGG		0.622	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		6	61	0	0	0	1	0	6	61				
TRPC4	7223	broad.mit.edu	37	13	38357494	38357494	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs12583681	byFrequency	TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr13:38357494G>A	ENST00000379705.3	-	0	834				TRPC4_ENST00000358477.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000338947.5_De_novo_Start_OutOfFrame|TRPC4_ENST00000379673.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000379679.1_5'Flank|TRPC4_ENST00000447043.1_De_novo_Start_OutOfFrame|TRPC4_ENST00000379681.3_De_novo_Start_OutOfFrame|TRPC4_ENST00000355779.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000426868.2_De_novo_Start_OutOfFrame			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CTATTTCTTCGTCTCTGAAAG	0.343													G|||	514	0.102636	0.0749	0.2061	5008	,	,		15979	0.0556		0.1511	False		,,,				2504	0.0654					ENST00000379705.3																			0				NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83								transient receptor potential cation channel, subfamily C, member 4		G	,,,,,	377,4029	188.1+/-214.6	15,347,1841	50.0	49.0	49.0		,,,,,	1.1	0.0	13	dbSNP_120	49	1266,7332	246.9+/-275.2	94,1078,3127	no	utr-5,utr-5,utr-5,utr-5,utr-5,utr-5	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	109,1425,4968	AA,AG,GG		14.7244,8.5565,12.6346	,,,,,	,,,,,	38357494	1643,11361	2203	4299	6502			7223				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity	g.chr13:38357494G>A	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.-24C>T	13.37:g.38357494G>A						TRPC4_ENST00000338947.5_De_novo_Start_OutOfFrame|TRPC4_ENST00000379673.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000379681.3_De_novo_Start_OutOfFrame|TRPC4_ENST00000358477.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000426868.2_De_novo_Start_OutOfFrame|TRPC4_ENST00000447043.1_De_novo_Start_OutOfFrame|TRPC4_ENST00000355779.2_De_novo_Start_OutOfFrame				Q9UBN4	TRPC4_HUMAN		all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)	0	834	-								B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Translation_Start_Site	SNP	ENST00000379705.3	37		CCDS9365.1																																																																																				0.343	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		3	24	0	0	0	1	0	3	24				
PNKP	11284	broad.mit.edu	37	19	50370414	50370414	+	Silent	SNP	A	A	G			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr19:50370414A>G	ENST00000322344.3	-	2	157	c.48T>C	c.(46-48)ccT>ccC	p.P16P	PNKP_ENST00000600573.1_Silent_p.P16P|PNKP_ENST00000600910.1_Silent_p.P16P|PNKP_ENST00000596014.1_Silent_p.P16P|PNKP_ENST00000595792.1_5'UTR	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	16	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)	p.P16P(8)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GCGCTCCCCCAGGGGGGCTCT	0.721								Other BER factors																														ENST00000322344.3																			8	Substitution - coding silent(8)	p.P16P(8)	lung(6)|urinary_tract(2)	breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19						c.(46-48)ccT>ccC	Other BER factors	polynucleotide kinase 3'-phosphatase							10.0	13.0	12.0					19																	50370414		2073	4105	6178	SO:0001819	synonymous_variant	11284				DNA damage response, detection of DNA damage|DNA-dependent DNA replication|nucleotide-excision repair, DNA damage removal|response to oxidative stress|response to radiation	nucleolus	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|damaged DNA binding|double-stranded DNA binding|endonuclease activity|nucleotide kinase activity|polynucleotide 3'-phosphatase activity|protein binding	g.chr19:50370414A>G	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.48T>C	19.37:g.50370414A>G						PNKP_ENST00000596014.1_Silent_p.P16P|PNKP_ENST00000600910.1_Silent_p.P16P|PNKP_ENST00000600573.1_Silent_p.P16P|PNKP_ENST00000595792.1_5'UTR	p.P16P	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)	2	157	-		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)	16					Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Silent	SNP	ENST00000322344.3	37	c.48T>C	CCDS12783.1																																																																																				0.721	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		9	25	0	0	0	1	0	9	25				
AMHR2	269	broad.mit.edu	37	12	53825209	53825209	+	Silent	SNP	C	C	T			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr12:53825209C>T	ENST00000257863.4	+	11	1754	c.1674C>T	c.(1672-1674)ggC>ggT	p.G558G	AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Silent_p.G463G	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	558					Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	TTCAGCAAGGCCCTTGTTCCA	0.517																																						ENST00000257863.4																			0				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34						c.(1672-1674)ggC>ggT		anti-Mullerian hormone receptor, type II	Adenosine triphosphate(DB00171)						138.0	115.0	123.0					12																	53825209		2203	4300	6503	SO:0001819	synonymous_variant	269				Mullerian duct regression		ATP binding|hormone binding|metal ion binding	g.chr12:53825209C>T	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"""Muellerian inhibiting substance type II receptor"""	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1674C>T	12.37:g.53825209C>T						AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Silent_p.G463G	p.G558G	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN			11	1754	+			558					A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Silent	SNP	ENST00000257863.4	37	c.1674C>T	CCDS8858.1																																																																																				0.517	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		11	95	0	0	0	1	0	11	95				
RSG1	79363	broad.mit.edu	37	1	16559499	16559499	+	Silent	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr1:16559499G>A	ENST00000375599.3	-	3	698	c.279C>T	c.(277-279)acC>acT	p.T93T		NM_030907.3	NP_112169.2	Q9BU20	RSG1_HUMAN	REM2 and RAB-like small GTPase 1	93	Small GTPase-like.				cellular protein localization (GO:0034613)|cilium assembly (GO:0042384)|exocytosis (GO:0006887)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle fusion (GO:0031338)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)	GTP binding (GO:0005525)			large_intestine(2)|lung(2)|pancreas(1)|prostate(1)	6						AAAATACCACGGTGGTCTGGA	0.552																																						ENST00000375599.3																			0				large_intestine(2)|lung(2)|pancreas(1)|prostate(1)	6						c.(277-279)acC>acT		REM2 and RAB-like small GTPase 1							75.0	79.0	78.0					1																	16559499		2203	4300	6503	SO:0001819	synonymous_variant	79363				cellular protein localization|cilium assembly|exocytosis|protein transport|regulation of exocytosis|regulation of vesicle fusion|small GTPase mediated signal transduction	cilium|microtubule basal body	GTP binding	g.chr1:16559499G>A	BC008702	CCDS171.1	1p36.13	2014-02-21	2011-02-22	2011-02-22	ENSG00000132881	ENSG00000132881			28127	protein-coding gene	gene with protein product	"""Rem/Rab-Similar GTPase 1"""		"""chromosome 1 open reading frame 89"""	C1orf89		19767740	Standard	NM_030907		Approved	MGC10731	uc001ayd.3	Q9BU20	OTTHUMG00000002214	ENST00000375599.3:c.279C>T	1.37:g.16559499G>A							p.T93T	NM_030907.3	NP_112169.2	Q9BU20	RSG1_HUMAN			3	698	-			93			Small GTPase-like.		Q5TEV7	Silent	SNP	ENST00000375599.3	37	c.279C>T	CCDS171.1																																																																																				0.552	RSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006279.2	NM_030907		11	71	0	0	0	1	0	11	71				
GOLGA4	2803	broad.mit.edu	37	3	37363363	37363363	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr3:37363363G>A	ENST00000361924.2	+	13	2061	c.1687G>A	c.(1687-1689)Gag>Aag	p.E563K	GOLGA4_ENST00000356847.4_Missense_Mutation_p.E585K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	563	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GCAAGAAGCAGAGACTTACAG	0.348																																						ENST00000361924.2																			0				NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(1687-1689)Gag>Aag		golgin A4							49.0	53.0	52.0					3																	37363363		2203	4299	6502	SO:0001583	missense	2803				Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding	g.chr3:37363363G>A	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1687G>A	3.37:g.37363363G>A	ENSP00000354486:p.Glu563Lys					GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.E585K	p.E563K	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN			13	2061	+			563			Glu-rich.		F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	c.1687G>A	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041572	0.93685	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000429018;ENST00000437131	T;T;T	0.31247	1.56;1.56;1.5	6.08	5.19	0.71726	.	0.000000	0.36932	N	0.002339	T	0.58736	0.2143	M	0.79475	2.455	0.50632	D	0.999885	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.83275	0.927;0.927;0.927;0.996	T	0.64373	-0.6423	10	0.62326	D	0.03	.	17.3022	0.87185	0.0:0.1254:0.8746:0.0	.	563;563;585;563	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	563;585;124;434	ENSP00000354486:E563K;ENSP00000349305:E585K;ENSP00000405842:E434K	ENSP00000349305:E585K	E	+	1	0	GOLGA4	37338367	1.000000	0.71417	0.987000	0.45799	0.967000	0.64934	7.256000	0.78350	1.546000	0.49388	0.655000	0.94253	GAG		0.348	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		5	32	0	0	0	1	0	5	32				
POU1F1	5449	broad.mit.edu	37	3	87325590	87325590	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr3:87325590G>A	ENST00000350375.2	-	1	147	c.23C>T	c.(22-24)tCg>tTg	p.S8L	POU1F1_ENST00000344265.3_Missense_Mutation_p.S8L|POU1F1_ENST00000560656.1_Missense_Mutation_p.S8L	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	8					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		GGTATCAGCCGAAGTAAAAGC	0.458																																						ENST00000350375.2																			0				central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18						c.(22-24)tCg>tTg		POU class 1 homeobox 1							90.0	92.0	91.0					3																	87325590		2203	4300	6503	SO:0001583	missense	5449				negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr3:87325590G>A	D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"""Homeoboxes / POU class"""	9210	protein-coding gene	gene with protein product	"""growth hormone factor 1"""	173110	"""POU domain class 1, transcription factor 1"""	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.23C>T	3.37:g.87325590G>A	ENSP00000263781:p.Ser8Leu					POU1F1_ENST00000560656.1_Missense_Mutation_p.S8L|POU1F1_ENST00000344265.3_Missense_Mutation_p.S8L	p.S8L	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)	1	147	-	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)	8					O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Missense_Mutation	SNP	ENST00000350375.2	37	c.23C>T	CCDS2919.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902062	0.92035	.	.	ENSG00000064835	ENST00000350375;ENST00000344265	T;T	0.67171	-0.25;-0.25	5.16	5.16	0.70880	.	869.327000	0.00166	N	0.000001	T	0.74007	0.3660	L	0.54323	1.7	0.42006	D	0.990912	D;P	0.54772	0.968;0.614	P;B	0.44860	0.462;0.041	T	0.67325	-0.5699	10	0.87932	D	0	.	19.0088	0.92863	0.0:0.0:1.0:0.0	.	8;8	P28069-2;P28069	.;PIT1_HUMAN	L	8	ENSP00000263781:S8L;ENSP00000342931:S8L	ENSP00000342931:S8L	S	-	2	0	POU1F1	87408280	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	5.254000	0.65457	2.559000	0.86315	0.591000	0.81541	TCG		0.458	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306		10	23	0	0	0	1	0	10	23				
PGF	5228	broad.mit.edu	37	14	75416122	75416122	+	Missense_Mutation	SNP	C	C	T	rs368317769		TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr14:75416122C>T	ENST00000405431.2	-	3	252	c.253G>A	c.(253-255)Ggc>Agc	p.G85S	PGF_ENST00000555567.1_Missense_Mutation_p.G85S|PGF_ENST00000238607.6_Missense_Mutation_p.G84S|PGF_ENST00000553716.1_Missense_Mutation_p.G85S			P49763	PLGF_HUMAN	placental growth factor	85					branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of morphogenesis of a branching structure (GO:0060688)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.00668)	Aflibercept(DB08885)	CCGCAGCAGCCGGTGCAGCGC	0.652																																					GBM(127;389 2301 5452 48547)	ENST00000555567.1																			0				kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8						c.(253-255)Ggc>Agc		placental growth factor		C	SER/GLY,SER/GLY	0,4406		0,0,2203	70.0	59.0	63.0		253,253	4.3	0.9	14		63	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PGF	NM_001207012.1,NM_002632.5	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	85/150,85/171	75416122	1,13005	2203	4300	6503	SO:0001583	missense	5228				angiogenesis|cell differentiation|cell-cell signaling|positive regulation of cell division|positive regulation of cell proliferation|vascular endothelial growth factor receptor signaling pathway	extracellular region|membrane	growth factor activity|heparin binding	g.chr14:75416122C>T	S72960	CCDS9835.1, CCDS55932.1, CCDS73664.1	14q24.3	2013-02-18	2008-03-20		ENSG00000119630	ENSG00000119630			8893	protein-coding gene	gene with protein product	"""placenta growth factor"""	601121	"""placental growth factor-like"", ""placental growth factor, vascular endothelial growth factor-related protein"""	PGFL		7681160	Standard	NM_002632		Approved	PLGF, PlGF-2, PlGF, SHGC-10760, D12S1900	uc001xqz.3	P49763	OTTHUMG00000171496	ENST00000405431.2:c.253G>A	14.37:g.75416122C>T	ENSP00000385365:p.Gly85Ser					PGF_ENST00000405431.2_Missense_Mutation_p.G85S|PGF_ENST00000553716.1_Missense_Mutation_p.G85S|PGF_ENST00000238607.6_Missense_Mutation_p.G84S	p.G85S	NM_002632.5	NP_002623.2	P49763	PLGF_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00668)	3	794	-			85					Q07101|Q9BV78|Q9Y6S8	Missense_Mutation	SNP	ENST00000405431.2	37	c.253G>A	CCDS9835.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522986	0.96431	0.0	1.16E-4	ENSG00000119630	ENST00000555567;ENST00000553716;ENST00000238607;ENST00000405431	.	.	.	4.33	4.33	0.51752	Platelet-derived growth factor, conserved site (1);Platelet-derived growth factor (PDGF) (3);	0.000000	0.85682	D	0.000000	D	0.85270	0.5658	M	0.91090	3.175	0.53005	D	0.999966	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.89297	0.3623	9	0.87932	D	0	.	16.6541	0.85224	0.0:1.0:0.0:0.0	.	85;85;84;85	P49763;P49763-2;G3XA84;Q53XY6	PLGF_HUMAN;.;.;.	S	85;85;84;85	.	ENSP00000238607:G85S	G	-	1	0	PGF	74485875	1.000000	0.71417	0.931000	0.37212	0.995000	0.86356	7.651000	0.83577	2.241000	0.73720	0.561000	0.74099	GGC		0.652	PGF-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414064.1	NM_002632		9	63	0	0	0	1	0	9	63				
JAM3	83700	broad.mit.edu	37	11	134018707	134018707	+	Silent	SNP	C	C	T	rs150992119		TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr11:134018707C>T	ENST00000299106.4	+	8	1050	c.891C>T	c.(889-891)gaC>gaT	p.D297D	JAM3_ENST00000441717.3_Silent_p.D246D|NCAPD3_ENST00000526787.2_5'Flank|JAM3_ENST00000529443.2_Silent_p.D342D			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	297					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		TCCGCACTGACGAGGAGGTAA	0.463																																						ENST00000299106.4																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10						c.(889-891)gaC>gaT		junctional adhesion molecule 3		C	,	2,4400	4.2+/-10.8	0,2,2199	69.0	65.0	67.0		738,891	-11.4	0.0	11	dbSNP_134	67	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	JAM3	NM_001205329.1,NM_032801.4	,	0,2,6496	TT,TC,CC		0.0,0.0454,0.0154	,	246/260,297/311	134018707	2,12994	2201	4297	6498	SO:0001819	synonymous_variant	83700				angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding	g.chr11:134018707C>T	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.891C>T	11.37:g.134018707C>T						JAM3_ENST00000441717.3_Silent_p.D246D|JAM3_ENST00000529443.2_Silent_p.D342D	p.D297D			Q9BX67	JAM3_HUMAN		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)	8	1050	+	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)	297					B3KWG9|Q8WWL8|Q96FL1	Silent	SNP	ENST00000299106.4	37	c.891C>T	CCDS8494.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.722	-0.783042	0.02907	4.54E-4	0.0	ENSG00000166086	ENST00000529443	.	.	.	6.04	-11.4	0.00090	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2596	0.37603	0.0:0.3689:0.1731:0.458	.	.	.	.	X	251	.	.	R	+	1	2	JAM3	133523917	0.072000	0.21174	0.028000	0.17463	0.082000	0.17680	-0.886000	0.04157	-2.598000	0.00452	-1.993000	0.00448	CGA		0.463	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		6	29	0	0	0	1	0	6	29				
RYR1	6261	broad.mit.edu	37	19	39026681	39026681	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr19:39026681G>A	ENST00000359596.3	+	82	11561	c.11561G>A	c.(11560-11562)gGg>gAg	p.G3854E	RYR1_ENST00000355481.4_Missense_Mutation_p.G3849E|RYR1_ENST00000360985.3_Missense_Mutation_p.G3854E|AC067969.2_ENST00000595853.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3854					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AAGGCCGAGGGGCTGGGCATG	0.577																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285						c.(11545-11547)gGg>gAg		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)						132.0	116.0	121.0					19																	39026681		2203	4300	6503	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:39026681G>A	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11561G>A	19.37:g.39026681G>A	ENSP00000352608:p.Gly3854Glu					RYR1_ENST00000359596.3_Missense_Mutation_p.G3854E|RYR1_ENST00000360985.3_Missense_Mutation_p.G3854E|AC067969.2_ENST00000595853.1_RNA	p.G3849E	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		81	11677	+	all_cancers(60;7.91e-06)		3854					Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.11546G>A	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.415270	0.42817	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.90261	-2.64;-2.64;-2.64	4.38	4.38	0.52667	.	0.075271	0.51477	U	0.000088	D	0.94843	0.8334	M	0.80746	2.51	0.49582	D	0.999804	D;D;D	0.69078	0.997;0.997;0.995	D;D;P	0.65987	0.94;0.94;0.873	D	0.95602	0.8664	10	0.87932	D	0	.	15.8873	0.79261	0.0:0.0:1.0:0.0	.	3854;3849;3854	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	E	3854;3849;3854	ENSP00000352608:G3854E;ENSP00000347667:G3849E;ENSP00000354254:G3854E	ENSP00000347667:G3849E	G	+	2	0	RYR1	43718521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.172000	0.94808	2.266000	0.75297	0.655000	0.94253	GGG		0.577	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			4	17	0	0	0	1	0	4	17				
RINT1	60561	broad.mit.edu	37	7	105177182	105177182	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr7:105177182C>G	ENST00000257700.2	+	3	490	c.259C>G	c.(259-261)Cag>Gag	p.Q87E		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	87					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AAGTAAAATGCAGTTAGAAGA	0.264																																						ENST00000257700.2																			0				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						c.(259-261)Cag>Gag		RAD50 interactor 1							59.0	58.0	59.0					7																	105177182		2203	4299	6502	SO:0001583	missense	60561				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding	g.chr7:105177182C>G	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.259C>G	7.37:g.105177182C>G	ENSP00000257700:p.Gln87Glu						p.Q87E	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN			3	490	+			87					Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	c.259C>G	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	C	9.725	1.160598	0.21454	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.22945	1.93	5.2	3.28	0.37604	.	0.545369	0.20693	N	0.087437	T	0.17492	0.0420	L	0.38175	1.15	0.31517	N	0.662884	B	0.13145	0.007	B	0.13407	0.009	T	0.29761	-1.0001	10	0.02654	T	1	-1.3121	13.1088	0.59261	0.4201:0.5799:0.0:0.0	.	87	Q6NUQ1	RINT1_HUMAN	E	87;56	ENSP00000257700:Q87E	ENSP00000257700:Q87E	Q	+	1	0	RINT1	104964418	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	1.864000	0.39469	0.494000	0.27859	0.491000	0.48974	CAG		0.264	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		4	21	0	0	0	1	0	4	21				
IMPDH1	3614	broad.mit.edu	37	7	128040207	128040207	+	Silent	SNP	C	C	T			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr7:128040207C>T	ENST00000480861.1	-	6	623	c.546G>A	c.(544-546)gtG>gtA	p.V182V	IMPDH1_ENST00000343214.4_Silent_p.V162V|IMPDH1_ENST00000338791.6_Silent_p.V272V|IMPDH1_ENST00000348127.6_Silent_p.V236V|IMPDH1_ENST00000470772.1_Silent_p.V186V|IMPDH1_ENST00000354269.5_Silent_p.V262V|IMPDH1_ENST00000496200.1_Silent_p.V162V|IMPDH1_ENST00000378717.4_Silent_p.V203V|IMPDH1_ENST00000419067.2_Silent_p.V239V	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						CTGCTGGAGCCACCACCAGTT	0.567																																						ENST00000338791.6																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						c.(814-816)gtG>gtA		IMP (inosine 5'-monophosphate) dehydrogenase 1	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)						166.0	156.0	160.0					7																	128040207		2203	4300	6503	SO:0001819	synonymous_variant	3614				GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding	g.chr7:128040207C>T		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.546G>A	7.37:g.128040207C>T						IMPDH1_ENST00000470772.1_Silent_p.V186V|IMPDH1_ENST00000496200.1_Silent_p.V162V|IMPDH1_ENST00000480861.1_Silent_p.V182V|IMPDH1_ENST00000419067.2_Silent_p.V239V|IMPDH1_ENST00000378717.4_Silent_p.V203V|IMPDH1_ENST00000354269.5_Silent_p.V262V|IMPDH1_ENST00000343214.4_Silent_p.V162V|IMPDH1_ENST00000348127.6_Silent_p.V236V	p.V272V	NM_000883.3	NP_000874.2	P20839	IMDH1_HUMAN			9	1166	-			187						Silent	SNP	ENST00000480861.1	37	c.816G>A	CCDS55161.1																																																																																				0.567	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883		21	129	0	0	0	1	0	21	129				
RRN3P2	653390	broad.mit.edu	37	16	29124405	29124405	+	RNA	SNP	C	C	T			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr16:29124405C>T	ENST00000564580.1	+	0	1483							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2																		CAGATGAAGACGAACCTGCTT	0.358																																						ENST00000564580.1																			0																																																			0							g.chr16:29124405C>T			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29124405C>T														0	1483	+									RNA	SNP	ENST00000564580.1	37																																																																																						0.358	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433243.1	NR_003369		4	19	0	0	0	1	0	4	19				
RINT1	60561	broad.mit.edu	37	7	105177177	105177177	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr7:105177177A>C	ENST00000257700.2	+	3	485	c.254A>C	c.(253-255)aAa>aCa	p.K85T		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	85					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						ACAGTAAGTAAAATGCAGTTA	0.284																																						ENST00000257700.2																			0				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						c.(253-255)aAa>aCa		RAD50 interactor 1							61.0	61.0	61.0					7																	105177177		2203	4299	6502	SO:0001583	missense	60561				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding	g.chr7:105177177A>C	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.254A>C	7.37:g.105177177A>C	ENSP00000257700:p.Lys85Thr						p.K85T	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN			3	485	+			85					Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	c.254A>C	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740465	0.69304	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.25579	1.79	5.2	5.2	0.72013	.	0.045171	0.85682	D	0.000000	T	0.32615	0.0835	L	0.55481	1.735	0.51767	D	0.999938	P	0.50443	0.935	P	0.49528	0.614	T	0.04621	-1.0938	10	0.18710	T	0.47	-10.6671	14.7113	0.69235	1.0:0.0:0.0:0.0	.	85	Q6NUQ1	RINT1_HUMAN	T	85;54	ENSP00000257700:K85T	ENSP00000257700:K85T	K	+	2	0	RINT1	104964413	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.052000	0.71080	1.953000	0.56701	0.402000	0.26972	AAA		0.284	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		4	24	0	0	0	1	0	4	24				
ANKRD52	283373	broad.mit.edu	37	12	56645997	56645997	+	Silent	SNP	A	A	G			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr12:56645997A>G	ENST00000267116.7	-	14	1594	c.1473T>C	c.(1471-1473)tcT>tcC	p.S491S		NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	491										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						AGTGGAGGGGAGAGCAGCCTT	0.577																																						ENST00000267116.7																			0				endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						c.(1471-1473)tcT>tcC		ankyrin repeat domain 52							96.0	103.0	101.0					12																	56645997		2077	4200	6277	SO:0001819	synonymous_variant	283373						protein binding	g.chr12:56645997A>G	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.1473T>C	12.37:g.56645997A>G							p.S491S	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN			14	1594	-			491					A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	37	c.1473T>C	CCDS44920.1																																																																																				0.577	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		12	87	0	0	0	1	0	12	87				
GGTLC1	92086	broad.mit.edu	37	20	23967157	23967157	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr20:23967157A>G	ENST00000335694.4	-	2	296	c.92T>C	c.(91-93)aTg>aCg	p.M31T	GGTLC1_ENST00000286890.4_Missense_Mutation_p.M31T|GGTLC1_ENST00000278765.4_Missense_Mutation_p.M31T	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	31					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)	p.M31T(6)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GTCATCCGGCATGTAGAACTC	0.622																																						ENST00000335694.4																			6	Substitution - Missense(6)	p.M31T(6)	lung(4)|NS(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						c.(91-93)aTg>aCg		gamma-glutamyltransferase light chain 1							67.0	61.0	63.0					20																	23967157		2203	4300	6503	SO:0001583	missense	92086						gamma-glutamyltransferase activity	g.chr20:23967157A>G	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.92T>C	20.37:g.23967157A>G	ENSP00000337587:p.Met31Thr					GGTLC1_ENST00000286890.4_Missense_Mutation_p.M31T|GGTLC1_ENST00000278765.4_Missense_Mutation_p.M31T	p.M31T	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN			2	296	-			31					D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	37	c.92T>C	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.745202	0.00087	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.05786	3.39;3.39;3.39	0.844	-1.69	0.08186	.	0.459428	0.22918	N	0.054055	T	0.01092	0.0036	N	0.00332	-1.63	0.20403	N	0.999909	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.02654	T	1	-29.1837	4.9338	0.13930	0.5039:0.0:0.4961:0.0	.	31	Q9BX51	GGTL1_HUMAN	T	31	ENSP00000286890:M31T;ENSP00000278765:M31T;ENSP00000337587:M31T	ENSP00000278765:M31T	M	-	2	0	GGTLC1	23915157	0.993000	0.37304	0.024000	0.17045	0.024000	0.10985	1.453000	0.35167	-1.885000	0.01118	-1.888000	0.00539	ATG		0.622	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		6	65	0	0	0	1	0	6	65				
PLXNA1	5361	broad.mit.edu	37	3	126707544	126707544	+	Silent	SNP	T	T	G			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr3:126707544T>G	ENST00000393409.2	+	1	108	c.108T>G	c.(106-108)ggT>ggG	p.G36G	PLXNA1_ENST00000251772.4_Silent_p.G13G	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	36	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.G13G(4)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CAGGCGGGGGTTCACAGCCCC	0.682																																						ENST00000251772.4																			4	Substitution - coding silent(4)	p.G13G(4)	lung(2)|kidney(2)	breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67						c.(37-39)ggT>ggG		plexin A1							26.0	27.0	27.0					3																	126707544		2203	4300	6503	SO:0001819	synonymous_variant	5361				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity	g.chr3:126707544T>G	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.108T>G	3.37:g.126707544T>G						PLXNA1_ENST00000393409.2_Silent_p.G36G	p.G13G			Q9UIW2	PLXA1_HUMAN		GBM - Glioblastoma multiforme(114;0.155)	1	108	+			36						Silent	SNP	ENST00000393409.2	37	c.39T>G	CCDS33847.2																																																																																				0.682	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		8	27	0	0	0	1	0	8	27				
MERTK	10461	broad.mit.edu	37	2	112777090	112777090	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr2:112777090G>A	ENST00000295408.4	+	16	2437	c.2180G>A	c.(2179-2181)cGa>cAa	p.R727Q	MERTK_ENST00000409780.1_Missense_Mutation_p.R551Q|MERTK_ENST00000421804.2_Missense_Mutation_p.R727Q			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	727	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						TTAGCTGCTCGAAACTGCATG	0.458																																						ENST00000295408.4																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						c.(2179-2181)cGa>cAa		c-mer proto-oncogene tyrosine kinase							136.0	127.0	130.0					2																	112777090		2203	4300	6503	SO:0001583	missense	10461				cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr2:112777090G>A	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2180G>A	2.37:g.112777090G>A	ENSP00000295408:p.Arg727Gln					MERTK_ENST00000421804.2_Missense_Mutation_p.R727Q|MERTK_ENST00000409780.1_Missense_Mutation_p.R551Q	p.R727Q			Q12866	MERTK_HUMAN			16	2437	+			727			Protein kinase.		Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	c.2180G>A	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	G	36	5.687545	0.96784	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000393237;ENST00000409780;ENST00000449344	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.3	5.3	0.74995	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.28146	U	0.016425	D	0.94584	0.8255	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95102	0.8231	10	0.87932	D	0	-17.8662	19.3044	0.94155	0.0:0.0:1.0:0.0	.	727	Q12866	MERTK_HUMAN	Q	727;727;363;551;34	ENSP00000295408:R727Q;ENSP00000389152:R727Q;ENSP00000387277:R551Q;ENSP00000412660:R34Q	ENSP00000295408:R727Q	R	+	2	0	MERTK	112493561	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.756000	0.98918	2.631000	0.89168	0.655000	0.94253	CGA		0.458	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			6	43	0	0	0	1	0	6	43				
SRP54-AS1	100506157	broad.mit.edu	37	14	35409214	35409214	+	RNA	SNP	T	T	C	rs1967723	byFrequency	TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr14:35409214T>C	ENST00000556355.1	-	0	257				RP11-85K15.2_ENST00000555015.1_RNA																							CAACTTCTAATTCATCTCGCC	0.448													C|||	1527	0.304912	0.2837	0.2824	5008	,	,		21625	0.37		0.2704	False		,,,				2504	0.318					ENST00000556355.1																			0																																																			0							g.chr14:35409214T>C																													14.37:g.35409214T>C						RP11-85K15.2_ENST00000555015.1_RNA								0	257	-									RNA	SNP	ENST00000556355.1	37																																																																																						0.448	RP11-85K15.2-004	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000410682.2			4	40	0	0	0	1	0	4	40				
CYP2B7P	1556	broad.mit.edu	37	19	41445086	41445086	+	RNA	SNP	G	G	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr19:41445086G>A	ENST00000599198.1	+	0	699					NR_001278.1															NS(1)|endometrium(6)|kidney(1)|lung(2)|ovary(1)|skin(1)	12						GAACATCCAGGACACACGAGA	0.537																																						ENST00000599198.1																			0				NS(1)|endometrium(6)|kidney(1)|lung(2)|ovary(1)|skin(1)	12																																														0							g.chr19:41445086G>A																													19.37:g.41445086G>A								NR_001278.1						0	699	+									RNA	SNP	ENST00000599198.1	37																																																																																						0.537	CYP2B7P1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000465180.1			2	2	0	0	0	1	0	2	2				
RINT1	60561	broad.mit.edu	37	7	105177178	105177178	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr7:105177178A>T	ENST00000257700.2	+	3	486	c.255A>T	c.(253-255)aaA>aaT	p.K85N		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	85					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CAGTAAGTAAAATGCAGTTAG	0.279																																						ENST00000257700.2																			0				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						c.(253-255)aaA>aaT		RAD50 interactor 1							61.0	60.0	61.0					7																	105177178		2203	4299	6502	SO:0001583	missense	60561				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding	g.chr7:105177178A>T	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.255A>T	7.37:g.105177178A>T	ENSP00000257700:p.Lys85Asn						p.K85N	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN			3	486	+			85					Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	c.255A>T	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.020589	0.54576	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.25250	1.81	5.2	5.2	0.72013	.	0.045171	0.85682	D	0.000000	T	0.19604	0.0471	L	0.44542	1.39	0.48901	D	0.999725	B	0.26902	0.163	B	0.20384	0.029	T	0.06215	-1.0839	10	0.22706	T	0.39	-10.6671	9.3027	0.37856	0.9183:0.0:0.0817:0.0	.	85	Q6NUQ1	RINT1_HUMAN	N	85;54	ENSP00000257700:K85N	ENSP00000257700:K85N	K	+	3	2	RINT1	104964414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.082000	0.41605	1.953000	0.56701	0.402000	0.26972	AAA		0.279	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		4	22	0	0	0	1	0	4	22				
TAB1	10454	broad.mit.edu	37	22	39814843	39814843	+	Silent	SNP	G	G	A	rs143506704	byFrequency	TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr22:39814843G>A	ENST00000216160.6	+	6	719	c.657G>A	c.(655-657)tcG>tcA	p.S219S	TAB1_ENST00000331454.3_Silent_p.S219S	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	219	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TCCGTCTTTCGCAGCTGGGTG	0.587													G|||	7	0.00139776	0.0	0.0	5008	,	,		20029	0.0		0.007	False		,,,				2504	0.0					ENST00000216160.6																			0				breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						c.(655-657)tcG>tcA		TGF-beta activated kinase 1/MAP3K7 binding protein 1		G	,	0,4406		0,0,2203	115.0	88.0	97.0		657,657	-9.8	0.6	22	dbSNP_134	97	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	TAB1	NM_006116.2,NM_153497.2	,	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	,	219/505,219/463	39814843	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	10454				activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane	catalytic activity|protein binding	g.chr22:39814843G>A	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.657G>A	22.37:g.39814843G>A						TAB1_ENST00000331454.3_Silent_p.S219S	p.S219S	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN			6	719	+			219			PP2C-like.		Q2PP09|Q8IZW2	Silent	SNP	ENST00000216160.6	37	c.657G>A	CCDS13993.1																																																																																				0.587	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		5	60	0	0	0	1	0	5	60				
IDH2	3418	broad.mit.edu	37	15	90631839	90631839	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr15:90631839T>A	ENST00000330062.3	-	4	627	c.514A>T	c.(514-516)Agg>Tgg	p.R172W	IDH2_ENST00000539790.1_Missense_Mutation_p.R42W|IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R120W	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172W(12)|p.R172G(2)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			TGGGCGTGCCTGCCAATGGTG	0.627			M		GBM																																	ENST00000330062.3				Dom	yes		15	15q26.1	3418	M	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """			M			GBM		14	Substitution - Missense(14)	p.R172W(12)|p.R172G(2)	central_nervous_system(9)|biliary_tract(5)	biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109						c.(514-516)Agg>Tgg		isocitrate dehydrogenase 2 (NADP+), mitochondrial							86.0	81.0	83.0					15																	90631839		2200	4298	6498	SO:0001583	missense	3418				2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding	g.chr15:90631839T>A		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.514A>T	15.37:g.90631839T>A	ENSP00000331897:p.Arg172Trp					IDH2_ENST00000559482.1_Intron|IDH2_ENST00000539790.1_Missense_Mutation_p.R42W|IDH2_ENST00000540499.2_Missense_Mutation_p.R120W	p.R172W	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)		4	627	-	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		172					B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	c.514A>T	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495142	0.44352	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.87029	-2.2;-2.2;-2.2	5.93	0.717	0.18196	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	H	0.98487	4.245	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.95508	0.8583	10	0.87932	D	0	.	13.7144	0.62687	0.0:0.0:0.4915:0.5085	.	172	P48735	IDHP_HUMAN	W	172;42;120	ENSP00000331897:R172W;ENSP00000438457:R42W;ENSP00000446147:R120W	ENSP00000331897:R172W	R	-	1	2	IDH2	88432843	1.000000	0.71417	0.032000	0.17829	0.002000	0.02628	1.525000	0.35953	-0.113000	0.11958	-0.466000	0.05196	AGG		0.627	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			9	57	0	0	0	1	0	9	57				
C16orf74	404550	broad.mit.edu	37	16	85743879	85743881	+	In_Frame_Del	DEL	GCT	GCT	-	rs374238893		TCGA-HT-7856-01A-11D-2395-08	TCGA-HT-7856-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe1d5590-b04f-4196-86f0-d3887c399996	36437e51-9b37-4436-919f-9a5e82f7cf8f	g.chr16:85743879_85743881delGCT	ENST00000284245.4	-	3	244_246	c.61_63delAGC	c.(61-63)agcdel	p.S21del	C16orf74_ENST00000602583.1_In_Frame_Del_p.S9del|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602758.1_Intron	NM_206967.2	NP_996850.1	Q96GX8	CP074_HUMAN	chromosome 16 open reading frame 74	21																	CCTCGTCGTGGCTGCTGCTGCTG	0.635																																						ENST00000602583.1																			0											c.(25-27)del		chromosome 16 open reading frame 74																																				SO:0001651	inframe_deletion	404550							g.chr16:85743879_85743881delGCT	BC009078	CCDS45540.1	16q24.1	2014-05-28			ENSG00000154102	ENSG00000154102			23362	protein-coding gene	gene with protein product							Standard	NM_206967		Approved	MGC17624	uc002fjc.4	Q96GX8	OTTHUMG00000183875	ENST00000284245.4:c.61_63delAGC	16.37:g.85743888_85743890delGCT	ENSP00000284245:p.Ser21del					C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000284245.4_In_Frame_Del_p.S21del|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602758.1_Intron|C16orf74_ENST00000602914.1_Intron	p.S9del			Q96GX8	CP074_HUMAN			1	575_577	-			21						In_Frame_Del	DEL	ENST00000284245.4	37	c.25_27delAGC	CCDS45540.1																																																																																				0.635	C16orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467253.1	NM_206967		2	4						2	4	---	---	---	---
