#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
CHRNA2	1135	broad.mit.edu	37	8	27319199	27319199	+	Missense_Mutation	SNP	A	A	G			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr8:27319199A>G	ENST00000520933.2	-	6	1690	c.1537T>C	c.(1537-1539)Ttc>Ctc	p.F513L	CHRNA2_ENST00000407991.1_Missense_Mutation_p.F513L|CHRNA2_ENST00000240132.2_Missense_Mutation_p.F498L			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	513					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GTCCCCAGGAAGCAGACGATG	0.572																																						ENST00000407991.1																			0				breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						c.(1537-1539)Ttc>Ctc		cholinergic receptor, nicotinic, alpha 2 (neuronal)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Doxacurium(DB01334)|Gallamine Triethiodide(DB00483)|Levallorphan(DB00504)|Mecamylamine(DB00657)|Metocurine Iodide(DB00416)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Rocuronium(DB00728)|Tubocurarine(DB01199)						279.0	221.0	241.0					8																	27319199		2203	4300	6503	SO:0001583	missense	0					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity	g.chr8:27319199A>G	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.1537T>C	8.37:g.27319199A>G	ENSP00000429616:p.Phe513Leu					CHRNA2_ENST00000520933.2_Missense_Mutation_p.F513L|CHRNA2_ENST00000240132.2_Missense_Mutation_p.F498L	p.F513L	NM_000742.3	NP_000733.2	Q15822	ACHA2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	7	2145	-		Ovarian(32;2.61e-05)	513					A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	c.1537T>C	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.233993	0.39498	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	D;D;D	0.83250	-1.7;-1.7;-1.7	5.69	3.36	0.38483	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.060823	0.64402	D	0.000002	T	0.54334	0.1852	N	0.01146	-0.985	0.38964	D	0.958608	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.006	T	0.45338	-0.9268	10	0.21014	T	0.42	.	6.2895	0.21051	0.7384:0.0:0.2616:0.0	.	498;513	B4DK19;Q15822	.;ACHA2_HUMAN	L	513;513;498	ENSP00000385026:F513L;ENSP00000429616:F513L;ENSP00000240132:F498L	ENSP00000240132:F498L	F	-	1	0	CHRNA2	27375116	0.970000	0.33590	1.000000	0.80357	0.913000	0.54294	0.452000	0.21795	0.992000	0.38840	0.459000	0.35465	TTC		0.572	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			17	41	0	0	0	1	0	17	41				
TRAFD1	10906	broad.mit.edu	37	12	112578720	112578720	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr12:112578720G>A	ENST00000257604.5	+	5	952	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	TRAFD1_ENST00000412615.2_Missense_Mutation_p.R112Q	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	112					negative regulation of innate immune response (GO:0045824)|response to cytokine (GO:0034097)		metal ion binding (GO:0046872)			kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						TGTGGTGCCCGGACGGAACTA	0.483																																						ENST00000257604.5																			0				kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						c.(334-336)cGg>cAg		TRAF-type zinc finger domain containing 1							119.0	106.0	110.0					12																	112578720		2203	4300	6503	SO:0001583	missense	10906				negative regulation of innate immune response	intracellular	protein binding|zinc ion binding	g.chr12:112578720G>A	AB007447	CCDS9160.1	12q24.13	2013-01-25			ENSG00000135148	ENSG00000135148			24808	protein-coding gene	gene with protein product		613197				12477932	Standard	NM_006700		Approved	FLN29	uc001ttp.3	O14545	OTTHUMG00000169640	ENST00000257604.5:c.335G>A	12.37:g.112578720G>A	ENSP00000257604:p.Arg112Gln					TRAFD1_ENST00000412615.2_Missense_Mutation_p.R112Q	p.R112Q	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN			5	952	+			112					A8K5L6|B4DI89	Missense_Mutation	SNP	ENST00000257604.5	37	c.335G>A	CCDS9160.1	.	.	.	.	.	.	.	.	.	.	G	35	5.569583	0.96540	.	.	ENSG00000135148	ENST00000412615;ENST00000549358;ENST00000257604;ENST00000552896	T;T;T;T	0.35236	1.32;1.32;1.32;1.32	5.92	5.92	0.95590	.	0.160039	0.52532	D	0.000061	T	0.65595	0.2706	M	0.81112	2.525	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.67268	-0.5713	10	0.72032	D	0.01	-21.6871	19.9191	0.97079	0.0:0.0:1.0:0.0	.	112;112	F8VNX8;O14545	.;TRAD1_HUMAN	Q	112	ENSP00000396526:R112Q;ENSP00000449319:R112Q;ENSP00000257604:R112Q;ENSP00000450357:R112Q	ENSP00000257604:R112Q	R	+	2	0	TRAFD1	111063103	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.233000	0.89799	2.812000	0.96745	0.563000	0.77884	CGG		0.483	TRAFD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405214.1	NM_006700		15	42	0	0	0	1	0	15	42				
HPDL	84842	broad.mit.edu	37	1	45793454	45793454	+	Silent	SNP	C	C	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr1:45793454C>T	ENST00000334815.3	+	1	910	c.634C>T	c.(634-636)Ctg>Ttg	p.L212L		NM_032756.2	NP_116145.1	Q96IR7	HPDL_HUMAN	4-hydroxyphenylpyruvate dioxygenase-like	212					aromatic amino acid family metabolic process (GO:0009072)		4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(166;0.155)					GCTTGGGGGACTGAGGCTTAC	0.642																																						ENST00000334815.3																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						c.(634-636)Ctg>Ttg		4-hydroxyphenylpyruvate dioxygenase-like							40.0	43.0	42.0					1																	45793454		2203	4299	6502	SO:0001819	synonymous_variant	84842				aromatic amino acid family metabolic process		4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding	g.chr1:45793454C>T	BC007293	CCDS519.1	1p34.1	2008-02-05	2007-03-14	2007-03-14	ENSG00000186603	ENSG00000186603			28242	protein-coding gene	gene with protein product			"""glyoxalase domain containing 1"""	GLOXD1		12477932	Standard	NM_032756		Approved	MGC15668, 4-HPPD-L	uc001cne.3	Q96IR7	OTTHUMG00000007681	ENST00000334815.3:c.634C>T	1.37:g.45793454C>T							p.L212L	NM_032756.2	NP_116145.1	Q96IR7	HPDL_HUMAN			1	910	+	Acute lymphoblastic leukemia(166;0.155)		212					B2R9B0	Silent	SNP	ENST00000334815.3	37	c.634C>T	CCDS519.1																																																																																				0.642	HPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020527.1	NM_032756		11	52	0	0	0	1	0	11	52				
SECISBP2L	9728	broad.mit.edu	37	15	49284490	49284490	+	Missense_Mutation	SNP	G	G	A	rs140688864	byFrequency	TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr15:49284490G>A	ENST00000559471.1	-	18	3520	c.3257C>T	c.(3256-3258)tCg>tTg	p.S1086L	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.S1041L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	1086							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTTGTTGAGCGAGCTGCAGTT	0.552													G|||	8	0.00159744	0.0	0.0	5008	,	,		18633	0.0079		0.0	False		,,,				2504	0.0					ENST00000559471.1																			0				breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						c.(3256-3258)tCg>tTg		SECIS binding protein 2-like		G	LEU/SER,LEU/SER	0,4394		0,0,2197	119.0	114.0	115.0		3257,3122	0.9	0.1	15	dbSNP_134	115	2,8588	2.2+/-6.3	0,2,4293	yes	missense,missense	SECISBP2L	NM_001193489.1,NM_014701.3	145,145	0,2,6490	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	1086/1102,1041/1057	49284490	2,12982	2197	4295	6492	SO:0001583	missense	9728							g.chr15:49284490G>A	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.3257C>T	15.37:g.49284490G>A	ENSP00000453854:p.Ser1086Leu					SECISBP2L_ENST00000261847.3_Missense_Mutation_p.S1041L	p.S1086L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN			18	3520	-			1086					Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	c.3257C>T	CCDS53942.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	G	6.925	0.540279	0.13250	0.0	2.33E-4	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.73897	-0.79	4.81	0.88	0.19161	.	0.904599	0.09397	N	0.807736	T	0.51278	0.1665	N	0.19112	0.55	0.26816	N	0.968889	B;B	0.12630	0.003;0.006	B;B	0.06405	0.001;0.002	T	0.49399	-0.8944	10	0.87932	D	0	.	9.3455	0.38107	0.2908:0.0:0.7092:0.0	.	1086;1041	Q93073;Q93073-2	SBP2L_HUMAN;.	L	1041;1086	ENSP00000261847:S1041L	ENSP00000261847:S1041L	S	-	2	0	SECISBP2L	47071782	0.843000	0.29541	0.073000	0.20177	0.018000	0.09664	1.042000	0.30303	0.015000	0.14971	-0.757000	0.03467	TCG		0.552	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		7	47	0	0	0	1	0	7	47				
HDDC3	374659	broad.mit.edu	37	15	91475311	91475311	+	Missense_Mutation	SNP	C	C	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr15:91475311C>T	ENST00000394272.3	-	2	170	c.142G>A	c.(142-144)Gga>Aga	p.G48R	UNC45A_ENST00000394275.2_Intron|HDDC3_ENST00000330334.3_Missense_Mutation_p.G48R|HDDC3_ENST00000559898.1_Missense_Mutation_p.G48R|AC068831.3_ENST00000438890.1_RNA|AC068831.3_ENST00000448987.1_RNA			Q8N4P3	MESH1_HUMAN	HD domain containing 3	48	HD.						guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity (GO:0008893)|metal ion binding (GO:0046872)			NS(1)|ovary(1)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TCAGTGATTCCCGCCTCGTGG	0.592											OREG0023475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000330334.3																			0				NS(1)|ovary(1)	2						c.(142-144)Gga>Aga		HD domain containing 3							50.0	50.0	50.0					15																	91475311		2198	4298	6496	SO:0001583	missense	374659						guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity|metal ion binding|phosphoric diester hydrolase activity	g.chr15:91475311C>T	AK057584	CCDS10366.1, CCDS66866.1	15q26.1	2005-08-22			ENSG00000184508	ENSG00000184508			30522	protein-coding gene	gene with protein product						12477932	Standard	NM_001286451		Approved	MGC45386	uc002bqe.4	Q8N4P3	OTTHUMG00000141260	ENST00000394272.3:c.142G>A	15.37:g.91475311C>T	ENSP00000377814:p.Gly48Arg		OREG0023475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1282	HDDC3_ENST00000394272.3_Missense_Mutation_p.G48R|UNC45A_ENST00000394275.2_Intron|HDDC3_ENST00000559898.1_Missense_Mutation_p.G48R	p.G48R	NM_198527.2	NP_940929.1	Q8N4P3	MESH1_HUMAN	Lung(145;0.189)		2	147	-	Lung NSC(78;0.0771)|all_lung(78;0.137)		48			HD.			Missense_Mutation	SNP	ENST00000394272.3	37	c.142G>A		.	.	.	.	.	.	.	.	.	.	C	32	5.184576	0.94885	.	.	ENSG00000184508	ENST00000394272;ENST00000330334	.	.	.	4.49	4.49	0.54785	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.110324	0.64402	D	0.000010	T	0.76300	0.3968	M	0.79926	2.475	0.58432	D	0.99999	D;D	0.56521	0.96;0.976	P;P	0.61003	0.882;0.852	T	0.77811	-0.2449	9	0.42905	T	0.14	-21.7715	14.0956	0.65019	0.0:1.0:0.0:0.0	.	48;48	Q8N4P3;Q8N4P3-2	MESH1_HUMAN;.	R	48	.	ENSP00000330721:G48R	G	-	1	0	HDDC3	89276315	0.999000	0.42202	0.999000	0.59377	0.983000	0.72400	6.363000	0.73082	2.334000	0.79466	0.555000	0.69702	GGA		0.592	HDDC3-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000280403.2	NM_198527		5	13	0	0	0	1	0	5	13				
ITGA9	3680	broad.mit.edu	37	3	37523045	37523045	+	Missense_Mutation	SNP	T	T	G			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr3:37523045T>G	ENST00000264741.5	+	4	747	c.491T>G	c.(490-492)aTc>aGc	p.I164S	ITGA9_ENST00000422441.1_Missense_Mutation_p.I164S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	164					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TTCTGCTACATCATCCCCTCC	0.537																																						ENST00000264741.5																			0				breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44						c.(490-492)aTc>aGc		integrin, alpha 9							249.0	208.0	222.0					3																	37523045		2203	4300	6503	SO:0001583	missense	3680				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity	g.chr3:37523045T>G	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.491T>G	3.37:g.37523045T>G	ENSP00000264741:p.Ile164Ser					ITGA9_ENST00000422441.1_Missense_Mutation_p.I164S	p.I164S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)	4	747	+			164					Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	c.491T>G	CCDS2669.1	.	.	.	.	.	.	.	.	.	.	T	15.15	2.748728	0.49257	.	.	ENSG00000144668	ENST00000422441;ENST00000264741	T;T	0.72725	-0.68;-0.68	5.47	5.47	0.80525	.	0.272209	0.40640	N	0.001048	T	0.65375	0.2685	L	0.45228	1.405	0.58432	D	0.999992	B;B	0.23591	0.043;0.088	B;B	0.25759	0.039;0.063	T	0.64837	-0.6313	10	0.66056	D	0.02	.	14.5203	0.67847	0.0:0.0:0.0:1.0	.	164;164	Q13797;E9PDS3	ITA9_HUMAN;.	S	164	ENSP00000397258:I164S;ENSP00000264741:I164S	ENSP00000264741:I164S	I	+	2	0	ITGA9	37498049	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	7.261000	0.78400	2.077000	0.62373	0.379000	0.24179	ATC		0.537	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		32	49	0	0	0	1	0	32	49				
TMCO3	55002	broad.mit.edu	37	13	114149937	114149937	+	Missense_Mutation	SNP	C	C	T	rs185071949	byFrequency	TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr13:114149937C>T	ENST00000434316.2	+	2	400	c.41C>T	c.(40-42)cCc>cTc	p.P14L	TMCO3_ENST00000375391.1_Missense_Mutation_p.P14L|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	14						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GTGCTGTTTCCCGTCCTTCCC	0.642													C|||	6	0.00119808	0.0	0.0	5008	,	,		15699	0.005		0.0	False		,,,				2504	0.001					ENST00000434316.2																			0				NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25						c.(40-42)cCc>cTc		transmembrane and coiled-coil domains 3							91.0	84.0	86.0					13																	114149937		2203	4300	6503	SO:0001583	missense	55002					integral to membrane	solute:hydrogen antiporter activity	g.chr13:114149937C>T	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.41C>T	13.37:g.114149937C>T	ENSP00000389399:p.Pro14Leu					TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Missense_Mutation_p.P14L	p.P14L	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	all cancers(43;0.0317)		2	400	+	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	14					Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	c.41C>T	CCDS9537.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	14.18	2.459064	0.43634	.	.	ENSG00000150403	ENST00000434316;ENST00000375391	T	0.28666	1.6	5.59	2.95	0.34219	.	0.506338	0.21058	N	0.080869	T	0.20129	0.0484	L	0.51422	1.61	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.14868	-1.0457	10	0.44086	T	0.13	-14.1903	10.5121	0.44868	0.0:0.795:0.0:0.205	.	14;14	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	L	14	ENSP00000389399:P14L	ENSP00000364540:P14L	P	+	2	0	TMCO3	113197938	0.113000	0.22115	0.000000	0.03702	0.003000	0.03518	1.500000	0.35682	0.340000	0.23745	0.650000	0.86243	CCC		0.642	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		5	25	0	0	0	1	0	5	25				
IFNL2	282616	broad.mit.edu	37	19	39759357	39759357	+	Silent	SNP	C	C	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr19:39759357C>T	ENST00000331982.5	+	2	106	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_172138.1	NP_742150.1	Q8IZJ0	IFNL2_HUMAN	interferon, lambda 2	17					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|mucosal immune response (GO:0002385)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											TGCTGATGGCCGCAGTGCTGA	0.637																																						ENST00000331982.5																			0											c.(49-51)gcC>gcT		interferon, lambda 2							54.0	58.0	57.0					19																	39759357		2199	4300	6499	SO:0001819	synonymous_variant	282616							g.chr19:39759357C>T	AY129148	CCDS42567.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000183709	ENSG00000183709		"""Interferons"""	18364	protein-coding gene	gene with protein product		607401	"""interleukin 28A"", ""interleukin 28A (interferon, lambda 2)"""	IL28A			Standard	NM_172138		Approved	IL-28A	uc002oku.1	Q8IZJ0		ENST00000331982.5:c.51C>T	19.37:g.39759357C>T							p.A17A	NM_172138.1	NP_742150.1					2	106	+								Q45KQ8|Q6VN55|Q8IWL7	Silent	SNP	ENST00000331982.5	37	c.51C>T	CCDS42567.1																																																																																				0.637	IFNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463833.1	NM_172138		7	44	0	0	0	1	0	7	44				
TMEM143	55260	broad.mit.edu	37	19	48866617	48866617	+	Missense_Mutation	SNP	G	G	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr19:48866617G>T	ENST00000293261.3	-	2	511	c.195C>A	c.(193-195)gaC>gaA	p.D65E	SYNGR4_ENST00000344846.2_5'Flank|TMEM143_ENST00000435956.3_Missense_Mutation_p.D65E|TMEM143_ENST00000436660.2_Missense_Mutation_p.D65E|TMEM143_ENST00000541566.1_Intron|TMEM143_ENST00000377431.2_Missense_Mutation_p.D65E|TMEM143_ENST00000598012.1_5'UTR	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	65					hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		GCTGGGCCCAGTCGCGGGGCT	0.667																																						ENST00000293261.3																			0				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14						c.(193-195)gaC>gaA		transmembrane protein 143							35.0	42.0	39.0					19																	48866617		2203	4298	6501	SO:0001583	missense	55260					integral to membrane|mitochondrion		g.chr19:48866617G>T	AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558			25603	protein-coding gene	gene with protein product						12975309	Standard	NM_018273		Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.195C>A	19.37:g.48866617G>T	ENSP00000293261:p.Asp65Glu					TMEM143_ENST00000541566.1_Intron|TMEM143_ENST00000598012.1_5'UTR|TMEM143_ENST00000436660.2_Missense_Mutation_p.D65E|TMEM143_ENST00000435956.3_Missense_Mutation_p.D65E|TMEM143_ENST00000377431.2_Missense_Mutation_p.D65E	p.D65E	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)	2	511	-		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)	65					A8K656|Q6UXY4|Q9NV49	Missense_Mutation	SNP	ENST00000293261.3	37	c.195C>A	CCDS12716.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004205	0.74932	.	.	ENSG00000161558	ENST00000293261;ENST00000377431;ENST00000435956;ENST00000436660	T;T	0.53857	0.72;0.6	5.56	0.861	0.19048	.	0.332477	0.27604	N	0.018625	T	0.35537	0.0935	N	0.24115	0.695	0.25190	N	0.990132	B;D;B;P;P	0.54207	0.003;0.965;0.031;0.682;0.457	B;P;B;B;B	0.47044	0.004;0.535;0.019;0.129;0.129	T	0.27088	-1.0084	10	0.62326	D	0.03	-7.255	1.825	0.03119	0.2283:0.1387:0.4901:0.143	.	65;65;65;65;65	B4DG49;B4DPF8;Q96AN5-2;B4DMT0;Q96AN5	.;.;.;.;TM143_HUMAN	E	65	ENSP00000293261:D65E;ENSP00000397038:D65E	ENSP00000293261:D65E	D	-	3	2	TMEM143	53558429	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	0.350000	0.20079	0.091000	0.17302	0.561000	0.74099	GAC		0.667	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465622.1	NM_018273		9	30	1	0	3.86212e-05	1	3.97247e-05	9	30				
IGKV1D-12	28903	broad.mit.edu	37	2	90198917	90198917	+	RNA	SNP	G	G	C			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr2:90198917G>C	ENST00000390276.2	+	0	259									immunoglobulin kappa variable 1D-12																		ACATCCAGATGACCCAGTCTC	0.458																																						ENST00000390276.2																			0																				90.0	122.0	113.0					2																	90198917		1456	4022	5478			0							g.chr2:90198917G>C	X17263		2p11.2	2014-05-06			ENSG00000240834	ENSG00000278857		"""Immunoglobulins / IGK locus"""	5746	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000188272		2.37:g.90198917G>C														0	259	+									RNA	SNP	ENST00000390276.2	37																																																																																						0.458	IGKV1D-12-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323139.2	NG_000833		11	55	0	0	0	1	0	11	55				
NEDD4	4734	broad.mit.edu	37	15	56142876	56142876	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr15:56142876G>A	ENST00000508342.1	-	10	2767	c.2468C>T	c.(2467-2469)tCc>tTc	p.S823F	NEDD4_ENST00000338963.2_Missense_Mutation_p.S751F|NEDD4_ENST00000435532.3_Missense_Mutation_p.S404F|NEDD4_ENST00000506154.1_Missense_Mutation_p.S807F	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	823	Mediates interaction with TNIK. {ECO:0000250}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		ATCACTGGTGGAGGCTTGTGA	0.498																																						ENST00000508342.1																			0				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						c.(2467-2469)tCc>tTc		neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase							81.0	81.0	81.0					15																	56142876		2193	4292	6485	SO:0001583	missense	4734				development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity	g.chr15:56142876G>A	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.2468C>T	15.37:g.56142876G>A	ENSP00000424827:p.Ser823Phe					NEDD4_ENST00000506154.1_Missense_Mutation_p.S807F|NEDD4_ENST00000338963.2_Missense_Mutation_p.S751F|NEDD4_ENST00000435532.3_Missense_Mutation_p.S404F	p.S823F			P46934	NEDD4_HUMAN		all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)	10	2767	-			823			Mediates interaction with TNIK (By similarity).		A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37	c.2468C>T		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.293|9.293	1.051035|1.051035	0.19827|0.19827	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	.|T;T;T;T	.|0.22539	.|1.95;2.03;1.97;1.96	5.19|5.19	1.21|1.21	0.21127|0.21127	.|.	.|5.588700	.|0.00166	.|N	.|0.000000	T|T	0.16811|0.16811	0.0404|0.0404	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.32101	.|0.019;0.323;0.356;0.137	.|B;B;B;B	.|0.41571	.|0.014;0.36;0.158;0.104	T|T	0.37244|0.37244	-0.9714|-0.9714	5|10	.|0.20046	.|T	.|0.44	.|.	9.2181|9.2181	0.37360|0.37360	0.2974:0.0:0.7026:0.0|0.2974:0.0:0.7026:0.0	.|.	.|807;404;823;751	.|P46934-2;P46934-4;P46934;P46934-3	.|.;.;NEDD4_HUMAN;.	S|F	414|823;404;751;807	.|ENSP00000424827:S823F;ENSP00000410613:S404F;ENSP00000345530:S751F;ENSP00000422705:S807F	.|ENSP00000345530:S751F	P|S	-|-	1|2	0|0	NEDD4|NEDD4	53930168|53930168	0.022000|0.022000	0.18835|0.18835	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	2.009000|2.009000	0.40903|0.40903	0.041000|0.041000	0.15688|0.15688	0.455000|0.455000	0.32223|0.32223	CCA|TCC		0.498	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		7	35	0	0	0	1	0	7	35				
PELI1	57162	broad.mit.edu	37	2	64323615	64323615	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr2:64323615G>A	ENST00000358912.4	-	5	875	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W		NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	145					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|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)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						GGAGGATTCCGTTCACATATG	0.373																																						ENST00000358912.4																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						c.(433-435)Cgg>Tgg		pellino E3 ubiquitin protein ligase 1							109.0	102.0	105.0					2																	64323615		2203	4300	6503	SO:0001583	missense	57162				innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol		g.chr2:64323615G>A		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.433C>T	2.37:g.64323615G>A	ENSP00000351789:p.Arg145Trp						p.R145W	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN			5	875	-			145					Q96SM0|Q9GZY5|Q9HCX0	Missense_Mutation	SNP	ENST00000358912.4	37	c.433C>T	CCDS1876.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753936	0.69648	.	.	ENSG00000197329	ENST00000358912	T	0.61510	0.1	5.5	3.69	0.42338	.	0.050782	0.85682	D	0.000000	T	0.76601	0.4010	M	0.88906	2.99	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	T	0.77803	-0.2451	10	0.87932	D	0	-16.7779	8.7163	0.34414	0.0688:0.0:0.6623:0.2689	.	145	Q96FA3	PELI1_HUMAN	W	145	ENSP00000351789:R145W	ENSP00000351789:R145W	R	-	1	2	PELI1	64177119	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.206000	0.42779	0.788000	0.33755	0.655000	0.94253	CGG		0.373	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651		5	17	0	0	0	1	0	5	17				
SIRPB1	10326	broad.mit.edu	37	20	1585397	1585397	+	Intron	SNP	T	T	C	rs148754551	byFrequency	TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr20:1585397T>C	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000381596.1_5'Flank|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|SIRPB1_ENST00000279477.7_Missense_Mutation_p.T248A	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.T248A(5)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTCGGATGGTCTCAGACAAG	0.627													t|||	2569	0.512979	0.6967	0.33	5008	,	,		3683	0.4435		0.4473	False		,,,				2504	0.5337					ENST00000279477.7																			5	Substitution - Missense(5)	p.T248A(5)	kidney(3)|prostate(2)	central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						c.(742-744)Acc>Gcc		signal-regulatory protein beta 1							20.0	30.0	27.0					20																	1585397		375	895	1270	SO:0001627	intron_variant	10326				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding	g.chr20:1585397T>C	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+15117A>G	20.37:g.1585397T>C						SIRPB1_ENST00000381605.4_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A	p.T248A	NM_001135844.2	NP_001129316.1	O00241	SIRB1_HUMAN			3	806	-			248					A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	c.742A>G	CCDS13019.1	757	0.3466117216117216	239	0.48577235772357724	97	0.26795580110497236	219	0.38286713286713286	202	0.26649076517150394	.	0.464	-0.887787	0.02511	.	.	ENSG00000101307	ENST00000279477	T	0.11930	2.73	2.24	-0.597	0.11653	.	.	.	.	.	T	0.00012	0.0000	N	0.20530	0.585	0.47778	P	4.809999999999537E-4	B	0.02656	0.0	B	0.06405	0.002	T	0.45483	-0.9258	8	0.13470	T	0.59	.	3.263	0.06855	0.2055:0.1485:0.0:0.646	.	248	Q5TFQ8	SIRBL_HUMAN	A	248	ENSP00000279477:T248A	ENSP00000279477:T248A	T	-	1	0	SIRPB1	1533397	0.001000	0.12720	0.631000	0.29282	0.161000	0.22273	-0.285000	0.08410	-0.814000	0.04352	-1.120000	0.02017	ACC		0.627	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		7	30	0	0	0	1	0	7	30				
RIN1	9610	broad.mit.edu	37	11	66103088	66103088	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr11:66103088G>A	ENST00000311320.4	-	4	574	c.448C>T	c.(448-450)Cac>Tac	p.H150Y	RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Missense_Mutation_p.H45Y|RIN1_ENST00000530056.1_Missense_Mutation_p.H45Y|RIN1_ENST00000524804.1_5'Flank	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	150	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CACCGGGTGTGGCAGTAGGCA	0.647																																						ENST00000311320.4																			0				breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						c.(448-450)Cac>Tac		Ras and Rab interactor 1							45.0	44.0	44.0					11																	66103088		2200	4295	6495	SO:0001583	missense	9610				endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding	g.chr11:66103088G>A	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.448C>T	11.37:g.66103088G>A	ENSP00000310406:p.His150Tyr					RIN1_ENST00000530056.1_Missense_Mutation_p.H45Y|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Missense_Mutation_p.H45Y	p.H150Y	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN			4	574	-			150			SH2.		O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	37	c.448C>T	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.170326	0.38315	.	.	ENSG00000174791	ENST00000311320;ENST00000424433;ENST00000530056	T;T;T	0.41758	0.99;1.56;1.56	3.81	3.81	0.43845	SH2 motif (3);	0.633137	0.14904	N	0.291643	T	0.24851	0.0603	N	0.14661	0.345	0.22521	N	0.999023	P;P	0.43826	0.818;0.666	B;B	0.43413	0.419;0.047	T	0.06734	-1.0810	10	0.02654	T	1	-8.5168	11.3956	0.49841	0.0:0.0:1.0:0.0	.	45;150	E9PNR2;Q13671	.;RIN1_HUMAN	Y	150;45;45	ENSP00000310406:H150Y;ENSP00000400560:H45Y;ENSP00000432798:H45Y	ENSP00000310406:H150Y	H	-	1	0	RIN1	65859664	0.278000	0.24230	0.970000	0.41538	0.950000	0.60333	0.528000	0.23002	2.144000	0.66660	0.462000	0.41574	CAC		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		6	14	0	0	0	1	0	6	14				
ARID2	196528	broad.mit.edu	37	12	46243462	46243462	+	Silent	SNP	A	A	G			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr12:46243462A>G	ENST00000334344.6	+	14	1987	c.1815A>G	c.(1813-1815)ccA>ccG	p.P605P	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Silent_p.P456P|ARID2_ENST00000444670.1_Silent_p.P215P	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	605					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GGGCTATACCACTTCCCATTC	0.463			"""N, S, F"""		hepatocellular carcinoma																																	ENST00000334344.6				Rec	yes		12	12q12	196528	"""N, S, F"""	AT rich interactive domain 2			E			hepatocellular carcinoma		0				NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116						c.(1813-1815)ccA>ccG		AT rich interactive domain 2 (ARID, RFX-like)							317.0	289.0	298.0					12																	46243462		2203	4300	6503	SO:0001819	synonymous_variant	196528				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding	g.chr12:46243462A>G		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1815A>G	12.37:g.46243462A>G						ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Silent_p.P456P|ARID2_ENST00000444670.1_Silent_p.P215P	p.P605P	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)	14	1987	+	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	605					Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	c.1815A>G	CCDS31783.1																																																																																				0.463	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		9	55	0	0	0	1	0	9	55				
LOC645752	645752	broad.mit.edu	37	15	78211171	78211171	+	lincRNA	SNP	A	A	G	rs12592262	byFrequency	TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr15:78211171A>G	ENST00000565869.1	+	0	111				RN7SL214P_ENST00000487317.2_RNA|RP11-114H24.2_ENST00000567226.1_RNA																							CTGGAAGAGCACGAGCCTCTC	0.602													-|||	2306	0.460463	0.3026	0.4452	5008	,	,		12449	0.7063		0.4433	False		,,,				2504	0.4489					ENST00000565869.1																			0																																																			0							g.chr15:78211171A>G																													15.37:g.78211171A>G						RP11-114H24.2_ENST00000567226.1_RNA								0	111	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.602	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			12	94	0	0	0	1	0	12	94				
SLC4A7	9497	broad.mit.edu	37	3	27444633	27444633	+	Missense_Mutation	SNP	T	T	C			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr3:27444633T>C	ENST00000295736.5	-	15	2361	c.2291A>G	c.(2290-2292)tAc>tGc	p.Y764C	SLC4A7_ENST00000428386.1_Missense_Mutation_p.Y640C|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000446700.1_Missense_Mutation_p.Y756C|SLC4A7_ENST00000454389.1_Missense_Mutation_p.Y773C|SLC4A7_ENST00000455077.1_Missense_Mutation_p.Y645C|SLC4A7_ENST00000440156.1_Missense_Mutation_p.Y760C|SLC4A7_ENST00000388777.4_Missense_Mutation_p.Y314C|SLC4A7_ENST00000445684.1_Missense_Mutation_p.Y760C|SLC4A7_ENST00000437179.1_Missense_Mutation_p.Y645C|SLC4A7_ENST00000435667.2_Missense_Mutation_p.Y649C	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	764					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	TACTTACGAGTAGCTGGTCAG	0.328																																						ENST00000295736.5																			0				NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38						c.(2290-2292)tAc>tGc		solute carrier family 4, sodium bicarbonate cotransporter, member 7							63.0	63.0	63.0					3																	27444633		2203	4300	6503	SO:0001583	missense	9497					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity	g.chr3:27444633T>C	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2291A>G	3.37:g.27444633T>C	ENSP00000295736:p.Tyr764Cys					SLC4A7_ENST00000388777.4_Missense_Mutation_p.Y314C|SLC4A7_ENST00000435667.2_Missense_Mutation_p.Y649C|SLC4A7_ENST00000440156.1_Missense_Mutation_p.Y760C|SLC4A7_ENST00000445684.1_Missense_Mutation_p.Y760C|SLC4A7_ENST00000437179.1_Missense_Mutation_p.Y645C|SLC4A7_ENST00000428386.1_Missense_Mutation_p.Y640C|SLC4A7_ENST00000454389.1_Missense_Mutation_p.Y773C|SLC4A7_ENST00000455077.1_Missense_Mutation_p.Y645C|SLC4A7_ENST00000446700.1_Missense_Mutation_p.Y756C|SLC4A7_ENST00000425128.2_3'UTR	p.Y764C	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN			15	2361	-			764					A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	c.2291A>G	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164417	0.78339	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29	5.43	5.43	0.79202	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91533	0.7326	M	0.92026	3.265	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0;0.995;0.998;1.0;0.999	D;D;D;D;D;D;D;D;D	0.97110	0.992;0.976;0.992;1.0;0.992;0.944;0.959;0.992;0.987	D	0.92815	0.6267	10	0.52906	T	0.07	.	15.466	0.75400	0.0:0.0:0.0:1.0	.	760;645;756;760;773;314;640;764;645	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	C	315;764;640;773;760;645;756;645;760;649;314;660	ENSP00000411031:Y315C;ENSP00000295736:Y764C;ENSP00000416368:Y640C;ENSP00000390394:Y773C;ENSP00000414797:Y760C;ENSP00000394252:Y645C;ENSP00000406605:Y756C;ENSP00000407382:Y645C;ENSP00000406804:Y760C;ENSP00000395336:Y649C;ENSP00000373429:Y314C;ENSP00000388703:Y660C	ENSP00000295736:Y764C	Y	-	2	0	SLC4A7	27419637	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.260000	0.72502	2.055000	0.61198	0.459000	0.35465	TAC		0.328	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		13	19	0	0	0	1	0	13	19				
PNPLA7	375775	broad.mit.edu	37	9	140358578	140358578	+	Splice_Site	SNP	C	C	T	rs201862577		TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr9:140358578C>T	ENST00000277531.4	-	27	3337	c.3151G>A	c.(3151-3153)Ggc>Agc	p.G1051S	PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000371457.1_Splice_Site_p.G657S|PNPLA7_ENST00000406427.1_Splice_Site_p.G1076S	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1051	Patatin.				lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GAGTGCTCACCGTCGGTGTGG	0.692																																						ENST00000406427.1																			0				breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						c.e28+1		patatin-like phospholipase domain containing 7							62.0	58.0	60.0					9																	140358578		2203	4300	6503	SO:0001630	splice_region_variant	375775				lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity	g.chr9:140358578C>T	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3151+1G>A	9.37:g.140358578C>T						PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000371457.1_Splice_Site_p.G657_splice|PNPLA7_ENST00000277531.4_Splice_Site_p.G1051_splice	p.G1076_splice	NM_001098537.1	NP_001092007.1	Q6ZV29	PLPL7_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)	28	3562	-	all_cancers(76;0.126)		1051			Patatin.		B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Splice_Site	SNP	ENST00000277531.4	37	c.3226_splice	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	c	23.0	4.363419	0.82353	.	.	ENSG00000130653	ENST00000371457;ENST00000371446;ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090	T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3	3.86	3.86	0.44501	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.000000	0.85682	D	0.000000	D	0.94745	0.8304	H	0.99897	4.91	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.80764	0.994;0.943;0.993;0.993	D	0.97273	0.9912	9	.	.	.	-28.3547	15.1359	0.72566	0.0:1.0:0.0:0.0	.	459;1076;1051;317	E2QRF8;Q6ZV29-5;Q6ZV29;B3KXH5	.;.;PLPL7_HUMAN;.	S	657;459;1051;1076;1051;1042	ENSP00000360512:G657S;ENSP00000360501:G459S;ENSP00000277531:G1051S;ENSP00000384610:G1076S;ENSP00000400582:G1042S	.	G	-	1	0	PNPLA7	139478399	1.000000	0.71417	0.845000	0.33349	0.319000	0.28217	7.419000	0.80179	1.855000	0.53841	0.457000	0.33378	GGC		0.692	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	Missense_Mutation	9	15	0	0	0	1	0	9	15				
CEP170B	283638	broad.mit.edu	37	14	105349547	105349547	+	Silent	SNP	T	T	C	rs200725057		TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr14:105349547T>C	ENST00000414716.3	+	8	981	c.753T>C	c.(751-753)gaT>gaC	p.D251D	CEP170B_ENST00000453495.1_Silent_p.D252D|CEP170B_ENST00000556508.1_Silent_p.D181D|CEP170B_ENST00000418279.1_Silent_p.D181D	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	251						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CCACGAAGGATGCAGAGGCAG	0.662													t|||	1	0.000199681	0.0	0.0	5008	,	,		12616	0.0		0.001	False		,,,				2504	0.0					ENST00000453495.1																			0											c.(754-756)gaT>gaC		centrosomal protein 170B			,	3,4053		0,3,2025	26.0	35.0	32.0		753,543	-3.4	0.0	14		32	16,8306		0,16,4145	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	0,19,6170	CC,CT,TT		0.1923,0.074,0.1535	,	251/1555,181/1520	105349547	19,12359	2028	4161	6189	SO:0001819	synonymous_variant	283638							g.chr14:105349547T>C	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.753T>C	14.37:g.105349547T>C						CEP170B_ENST00000418279.1_Silent_p.D181D|CEP170B_ENST00000414716.3_Silent_p.D251D|CEP170B_ENST00000556508.1_Silent_p.D181D	p.D252D							8	984	+								Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	c.756T>C	CCDS45175.1																																																																																				0.662	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		6	32	0	0	0	1	0	6	32				
KEAP1	9817	broad.mit.edu	37	19	10610400	10610400	+	Missense_Mutation	SNP	T	T	C			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr19:10610400T>C	ENST00000171111.5	-	2	857	c.310A>G	c.(310-312)Agc>Ggc	p.S104G	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.S104G	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	104	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	AAGACAGGGCTGGATGAGGCC	0.622																																						ENST00000171111.5																			0				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92						c.(310-312)Agc>Ggc		kelch-like ECH-associated protein 1							82.0	67.0	72.0					19																	10610400		2203	4300	6503	SO:0001583	missense	9817				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding	g.chr19:10610400T>C	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.310A>G	19.37:g.10610400T>C	ENSP00000171111:p.Ser104Gly					KEAP1_ENST00000393623.2_Missense_Mutation_p.S104G	p.S104G	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		2	857	-			104			BTB.		B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	37	c.310A>G	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.488221	0.44249	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	D;D	0.85629	-2.01;-2.01	4.68	4.68	0.58851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.099963	0.64402	D	0.000004	D	0.94345	0.8182	H	0.96111	3.77	0.51012	D	0.999903	D	0.89917	1.0	D	0.87578	0.998	D	0.95452	0.8535	10	0.87932	D	0	.	12.0934	0.53739	0.0:0.0:0.0:1.0	.	104	Q14145	KEAP1_HUMAN	G	104	ENSP00000171111:S104G;ENSP00000377245:S104G	ENSP00000171111:S104G	S	-	1	0	KEAP1	10471400	1.000000	0.71417	0.996000	0.52242	0.139000	0.21198	5.064000	0.64338	1.756000	0.51951	0.379000	0.24179	AGC		0.622	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		13	6	0	0	0	1	0	13	6				
FBXL18	80028	broad.mit.edu	37	7	5529772	5529772	+	Missense_Mutation	SNP	G	G	C			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr7:5529772G>C	ENST00000453700.3	-	5	2189	c.2072C>G	c.(2071-2073)tCt>tGt	p.S691C	FBXL18_ENST00000382368.3_Intron			Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	691									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		AGTGGCTCGAGACGTCCTGGC	0.617																																						ENST00000453700.3																		FBXL18/RNF216(2)	0				central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21						c.(2071-2073)tCt>tGt		F-box and leucine-rich repeat protein 18							20.0	20.0	20.0					7																	5529772		875	1990	2865	SO:0001583	missense	80028							g.chr7:5529772G>C	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000453700.3:c.2072C>G	7.37:g.5529772G>C	ENSP00000444797:p.Ser691Cys					FBXL18_ENST00000382368.3_Intron	p.S691C			Q96ME1	FXL18_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)	5	2189	-		Ovarian(82;0.0607)	691					Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000453700.3	37	c.2072C>G		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.648|7.648	0.682222|0.682222	0.14907|0.14907	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000458142|ENST00000312577;ENST00000453700	.|T	.|0.50548	.|0.74	1.55|1.55	1.55|1.55	0.23275|0.23275	.|.	.|.	.|.	.|.	.|.	T|T	0.30293|0.30293	0.0760|0.0760	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|P	.|0.49185	.|0.92	.|B	.|0.34652	.|0.187	T|T	0.23332|0.23332	-1.0191|-1.0191	4|8	.|0.87932	.|D	.|0	.|.	6.5603|6.5603	0.22483|0.22483	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|691	.|F5H4Z4	.|.	V|C	575|691	.|ENSP00000444797:S691C	.|ENSP00000311990:S691C	L|S	-|-	1|2	0|0	FBXL18|FBXL18	5496298|5496298	0.005000|0.005000	0.15991|0.15991	0.003000|0.003000	0.11579|0.11579	0.004000|0.004000	0.04260|0.04260	1.576000|1.576000	0.36504|0.36504	1.217000|1.217000	0.43442|0.43442	0.313000|0.313000	0.20887|0.20887	CTC|TCT		0.617	FBXL18-201	KNOWN	basic	protein_coding	protein_coding		NM_024963		9	7	0	0	0	1	0	9	7				
ZNF454	285676	broad.mit.edu	37	5	178392106	178392106	+	Missense_Mutation	SNP	A	A	G			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr5:178392106A>G	ENST00000320129.3	+	5	1004	c.701A>G	c.(700-702)cAc>cGc	p.H234R	ZNF454_ENST00000519564.1_Missense_Mutation_p.H234R	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		CTTATCCATCACCAAAGAATT	0.388																																						ENST00000320129.3																			0				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46						c.(700-702)cAc>cGc		zinc finger protein 454							99.0	103.0	101.0					5																	178392106		2203	4300	6503	SO:0001583	missense	285676				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr5:178392106A>G	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.701A>G	5.37:g.178392106A>G	ENSP00000326249:p.His234Arg					ZNF454_ENST00000519564.1_Missense_Mutation_p.H234R	p.H234R	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)	5	1004	+	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	234					Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	c.701A>G	CCDS4441.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.19|16.19	3.053062|3.053062	0.55218|0.55218	.|.	.|.	ENSG00000178187|ENSG00000113262	ENST00000320129;ENST00000519564|ENST00000319065	D;D|.	0.86865|.	-2.18;-2.18|.	4.46|4.46	4.46|4.46	0.54185|0.54185	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.000000|.	0.41823|.	D|.	0.000813|.	T|T	0.80037|0.80037	0.4550|0.4550	M|M	0.93678|0.93678	3.445|3.445	0.37782|0.37782	D|D	0.927065|0.927065	D|.	0.76494|.	0.999|.	D|.	0.65684|.	0.937|.	D|D	0.85097|0.85097	0.0955|0.0955	10|6	0.87932|0.87932	D|D	0|0	-14.7734|-14.7734	8.3346|8.3346	0.32206|0.32206	0.8001:0.1999:0.0:0.0|0.8001:0.1999:0.0:0.0	.|.	234|.	Q8N9F8|.	ZN454_HUMAN|.	R|A	234|1088	ENSP00000326249:H234R;ENSP00000430354:H234R|.	ENSP00000326249:H234R|ENSP00000325675:V1088A	H|V	+|-	2|2	0|0	ZNF454|GRM6	178324712|178324712	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	8.342000|8.342000	0.90049|0.90049	1.999000|1.999000	0.58509|0.58509	0.454000|0.454000	0.30748|0.30748	CAC|GTG		0.388	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		21	46	0	0	0	1	0	21	46				
CASR	846	broad.mit.edu	37	3	121980815	121980815	+	Silent	SNP	C	C	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr3:121980815C>T	ENST00000490131.1	+	4	1305	c.933C>T	c.(931-933)ttC>ttT	p.F311F	CASR_ENST00000296154.5_Silent_p.F311F|CASR_ENST00000498619.1_Silent_p.F311F	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	311					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CTCAGTACTTCCACGTGGTTG	0.597																																						ENST00000498619.1																			0				NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						c.(931-933)ttC>ttT		calcium-sensing receptor	Cinacalcet(DB01012)						62.0	55.0	57.0					3																	121980815		2203	4300	6503	SO:0001819	synonymous_variant	846				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity	g.chr3:121980815C>T	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.933C>T	3.37:g.121980815C>T						CASR_ENST00000490131.1_Silent_p.F311F|CASR_ENST00000296154.5_Silent_p.F311F	p.F311F	NM_001178065.1	NP_001171536.1	P41180	CASR_HUMAN		GBM - Glioblastoma multiforme(114;0.226)	4	1371	+			311					Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Silent	SNP	ENST00000490131.1	37	c.933C>T	CCDS3010.1																																																																																				0.597	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		20	36	0	0	0	1	0	20	36				
PLIN5	440503	broad.mit.edu	37	19	4523662	4523662	+	Missense_Mutation	SNP	T	T	C			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr19:4523662T>C	ENST00000381848.3	-	8	1350	c.1270A>G	c.(1270-1272)Agg>Ggg	p.R424G		NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	424	Interaction with PNPLA2 and ABHD5. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						CTCCCGTCCCTGTGCTCTGCC	0.701											OREG0025168	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000381848.3																			0				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						c.(1270-1272)Agg>Ggg		perilipin 5							68.0	77.0	74.0					19																	4523662		2005	4167	6172	SO:0001583	missense	440503					lipid particle		g.chr19:4523662T>C	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.1270A>G	19.37:g.4523662T>C	ENSP00000371272:p.Arg424Gly		OREG0025168	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	619		p.R424G	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN			8	1350	-			424					A2RRC1|Q6ZS68	Missense_Mutation	SNP	ENST00000381848.3	37	c.1270A>G	CCDS42473.1	.	.	.	.	.	.	.	.	.	.	T	2.595	-0.294309	0.05568	.	.	ENSG00000214456	ENST00000381848	T	0.12147	2.71	4.62	1.17	0.20885	.	5.447750	0.01386	U	0.013110	T	0.05593	0.0147	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33650	-0.9860	10	0.07990	T	0.79	-7.6457	6.5387	0.22369	0.0:0.5475:0.3514:0.1011	.	424	Q00G26	PLIN5_HUMAN	G	424	ENSP00000371272:R424G	ENSP00000371272:R424G	R	-	1	2	PLIN5	4474662	0.001000	0.12720	0.002000	0.10522	0.007000	0.05969	-0.115000	0.10741	0.038000	0.15604	-0.385000	0.06624	AGG		0.701	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706		9	79	0	0	0	1	0	9	79				
FFAR1	2864	broad.mit.edu	37	19	35842863	35842863	+	Missense_Mutation	SNP	C	C	T			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr19:35842863C>T	ENST00000246553.2	+	1	419	c.409C>T	c.(409-411)Cac>Tac	p.H137Y		NM_005303.2	NP_005294.1	O14842	FFAR1_HUMAN	free fatty acid receptor 1	137					energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|positive regulation of GTPase activity (GO:0043547)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Icosapent(DB00159)	CGTCCTGTGTCACCTGGGTCT	0.657																																						ENST00000246553.2																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						c.(409-411)Cac>Tac		free fatty acid receptor 1	Icosapent(DB00159)						78.0	77.0	77.0					19																	35842863		2203	4300	6503	SO:0001583	missense	2864				energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane	G-protein coupled receptor activity|guanyl-nucleotide exchange factor activity|lipid binding	g.chr19:35842863C>T	AF024687	CCDS12458.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000126266	ENSG00000126266		"""GPCR / Class A : Fatty acid receptors"""	4498	protein-coding gene	gene with protein product		603820	"""G protein-coupled receptor 40"""	GPR40		15684720	Standard	NM_005303		Approved	FFA1R	uc002nzc.2	O14842		ENST00000246553.2:c.409C>T	19.37:g.35842863C>T	ENSP00000246553:p.His137Tyr						p.H137Y	NM_005303.2	NP_005294.1	O14842	FFAR1_HUMAN	Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		1	419	+	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		137					Q0VAS2|Q4VBL4	Missense_Mutation	SNP	ENST00000246553.2	37	c.409C>T	CCDS12458.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.209031	0.58343	.	.	ENSG00000126266	ENST00000246553	T	0.71461	-0.57	4.23	4.23	0.50019	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.77538	0.4145	L	0.61218	1.895	0.37694	D	0.923947	D	0.76494	0.999	D	0.77004	0.989	T	0.75288	-0.3370	10	0.02654	T	1	-22.784	14.1376	0.65297	0.0:1.0:0.0:0.0	.	137	O14842	FFAR1_HUMAN	Y	137	ENSP00000246553:H137Y	ENSP00000246553:H137Y	H	+	1	0	FFAR1	40534703	1.000000	0.71417	1.000000	0.80357	0.481000	0.33189	6.386000	0.73186	2.171000	0.68590	0.561000	0.74099	CAC		0.657	FFAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466112.2	NM_005303		16	48	0	0	0	1	0	16	48				
CHSY1	22856	broad.mit.edu	37	15	101775489	101775489	+	Missense_Mutation	SNP	T	T	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr15:101775489T>A	ENST00000254190.3	-	2	1089	c.614A>T	c.(613-615)gAa>gTa	p.E205V		NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	205					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCCCATTTCTTCCGTGGTGCC	0.587																																						ENST00000254190.3																			0				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24						c.(613-615)gAa>gTa		chondroitin sulfate synthase 1							47.0	45.0	46.0					15																	101775489		2203	4300	6503	SO:0001583	missense	22856				chondroitin sulfate biosynthetic process	Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity	g.chr15:101775489T>A	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.614A>T	15.37:g.101775489T>A	ENSP00000254190:p.Glu205Val						p.E205V	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)		2	1089	-	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		205					Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	37	c.614A>T	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	T	31	5.085618	0.94100	.	.	ENSG00000131873	ENST00000254190	D	0.84516	-1.86	5.72	5.72	0.89469	.	0.127938	0.50627	D	0.000106	D	0.88149	0.6359	M	0.81112	2.525	0.80722	D	1	P	0.37985	0.613	B	0.42282	0.382	D	0.88958	0.3391	10	0.59425	D	0.04	-25.6699	16.0204	0.80478	0.0:0.0:0.0:1.0	.	205	Q86X52	CHSS1_HUMAN	V	205	ENSP00000254190:E205V	ENSP00000254190:E205V	E	-	2	0	CHSY1	99593012	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.187000	0.72039	2.174000	0.68829	0.533000	0.62120	GAA		0.587	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918		9	38	0	0	0	1	0	9	38				
EFCAB14	9813	broad.mit.edu	37	1	47182006	47182007	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr1:47182006_47182007insAA	ENST00000371933.3	-	2	1270_1271	c.294_295insTT	c.(292-297)ctcaagfs	p.K99fs	EFCAB14_ENST00000544071.1_Frame_Shift_Ins_p.K99fs	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	99							calcium ion binding (GO:0005509)										AGATCCTCCTTGAGAGCAACCT	0.421																																						ENST00000371933.3																			0											c.(292-297)ctaggafs		EF-hand calcium binding domain 14																																				SO:0001589	frameshift_variant	9813							g.chr1:47182006_47182007insAA	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.294_295insTT	1.37:g.47182006_47182007insAA	ENSP00000361001:p.Lys99fs					EFCAB14_ENST00000544071.1_Frame_Shift_Ins_p.G99fs	p.G99fs	NM_014774.2	NP_055589.1					2	1270_1271	-								D3DQ23|Q5SXB8	Frame_Shift_Ins	INS	ENST00000371933.3	37	c.294_295insTT	CCDS30706.1																																																																																				0.421	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		14	32						14	32	---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72280990	72280991	+	RNA	DEL	AC	AC	-	rs6960315		TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr7:72280990_72280991delAC	ENST00000435769.2	-	0	555				TYW1B_ENST00000438904.2_RNA|TYW1B_ENST00000438125.1_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)						tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)										gtgtgtgtgtacgtgtgtgtgc	0.381																																						ENST00000438125.1																			0													tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)																																						441250				tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity	g.chr7:72280990_72280991delAC	BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149			33908	protein-coding gene	gene with protein product	"""radical S-adenosyl methionine and flavodoxin domains 1"", ""non-protein coding RNA 69"", ""long intergenic non-protein coding RNA 69"""		"""tRNA-yW synthesizing protein 1 homolog B (non-protein coding)"""				Standard	NM_001145440		Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067		7.37:g.72280990_72280991delAC										Q6NUM6	TYW1B_HUMAN			0	336	-								A6NG09|B4DFY2|Q3KQX2	RNA	DEL	ENST00000435769.2	37																																																																																						0.381	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347346.2	NM_001145440		7	72						7	72	---	---	---	---
TRBV7-7	28591	broad.mit.edu	37	7	142120209	142120210	+	RNA	DEL	TG	TG	-			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr7:142120209_142120210delTG	ENST00000390377.1	-	0	49									T cell receptor beta variable 7-7																		cagacacacatgcatacacaca	0.436																																						ENST00000390377.1																			0																																																			0							g.chr7:142120209_142120210delTG	L36092		7q34	2012-02-07			ENSG00000253291	ENSG00000253291		"""T cell receptors / TRB locus"""	12241	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV77, TCRBV6S6A2T, TCRBV7S7			OTTHUMG00000158872		7.37:g.142120209_142120210delTG														0	49	-									RNA	DEL	ENST00000390377.1	37																																																																																						0.436	TRBV7-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000352480.1	NG_001333		7	126						7	126	---	---	---	---
MIRLET7DHG	158257	broad.mit.edu	37	9	96941099	96941100	+	lincRNA	INS	-	-	A			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr9:96941099_96941100insA	ENST00000602652.1	+	0	2870				MIRLET7F1_ENST00000362202.1_RNA|MIRLET7D_ENST00000362263.1_RNA|MIRLET7DHG_ENST00000416309.2_lincRNA|RP11-2B6.3_ENST00000602703.1_lincRNA|MIRLET7A1_ENST00000362295.2_RNA																							AGACCAGCAAGAAAAAAAAAAT	0.376																																						ENST00000416309.2																			0																																																			0							g.chr9:96941099_96941100insA																													9.37:g.96941109_96941109dupA						RP11-2B6.3_ENST00000602703.1_lincRNA		NR_046163.1						0	164	-									RNA	INS	ENST00000602652.1	37																																																																																						0.376	RP11-2B6.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000467606.1			2	4						2	4	---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14284600	14284600	+	RNA	DEL	A	A	-	rs79477301		TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr11:14284600delA	ENST00000534587.1	-	0	38				SPON1_ENST00000310358.7_RNA																							GGACCTGTTTaaaaaaaaaaa	0.463																																						ENST00000310358.7																			0				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21								spondin 1, extracellular matrix protein																																						10418				cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding	g.chr11:14284600delA																													11.37:g.14284600delA						RP11-21L19.1_ENST00000534587.1_RNA				Q9HCB6	SPON1_HUMAN		Epithelial(150;0.00898)	0	2795	+									RNA	DEL	ENST00000534587.1	37																																																																																						0.463	RP11-21L19.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000386031.1			3	4						3	4	---	---	---	---
EIF3CL	728689	broad.mit.edu	37	16	28403353	28403355	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-FY-A4B0-01A-21D-A23U-08	TCGA-FY-A4B0-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c5369c0-0005-4ca1-b5c7-0f44174f556b	fadf7923-0df0-4bd1-bc7a-707eb8181477	g.chr16:28403353_28403355delTCC	ENST00000398943.3	-	9	1021_1023	c.885_887delGGA	c.(883-888)gaggac>gac	p.E295del	EIF3CL_ENST00000398944.3_In_Frame_Del_p.E295del|EIF3CL_ENST00000380876.4_In_Frame_Del_p.E295del			B5ME19	EIFCL_HUMAN	eukaryotic translation initiation factor 3, subunit C-like	295					formation of translation preinitiation complex (GO:0001731)|regulation of translational initiation (GO:0006446)	eukaryotic 43S preinitiation complex (GO:0016282)|eukaryotic 48S preinitiation complex (GO:0033290)|eukaryotic translation initiation factor 3 complex (GO:0005852)	translation initiation factor activity (GO:0003743)										GCCTTCATTGTCCTCCTCCTCCT	0.547																																						ENST00000398943.3																			0											c.(883-888)gac>ga		eukaryotic translation initiation factor 3, subunit C-like																																				SO:0001651	inframe_deletion	728689							g.chr16:28403353_28403355delTCC		CCDS42136.1	16p11.2	2008-10-28			ENSG00000205609	ENSG00000205609			26347	protein-coding gene	gene with protein product							Standard	NM_001099661		Approved			B5ME19	OTTHUMG00000097025	ENST00000398943.3:c.885_887delGGA	16.37:g.28403362_28403364delTCC	ENSP00000381916:p.Glu295del					EIF3CL_ENST00000380876.4_In_Frame_Del_p.ED295del|EIF3CL_ENST00000398944.3_In_Frame_Del_p.ED295del	p.ED295del							9	1021_1023	-									In_Frame_Del	DEL	ENST00000398943.3	37	c.885_887delGGA	CCDS42136.1																																																																																				0.547	EIF3CL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214116.1			7	12						7	12	---	---	---	---
