#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
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	lincRNA	SNP	A	A	G	rs374719458		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373																																						ENST00000548109.1																			0																																																			0							g.chr14:19857036A>G																													14.37:g.19857036A>G														0	72	+									RNA	SNP	ENST00000548109.1	37																																																																																						0.373	RP11-146E13.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000409408.1			5	30	0	0	0	1	0	5	30				
PIEZO1	9780	broad.mit.edu	37	16	88779765	88779765	+	IGR	SNP	G	G	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr16:88779765G>T	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.K261N|CTU2_ENST00000567949.1_Missense_Mutation_p.K332N|CTU2_ENST00000378384.3_Missense_Mutation_p.K174N|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.K261N	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GCTACTCCAAGGTCATGACTG	0.657																																						ENST00000567949.1																			0				NS(1)|breast(1)|endometrium(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11						c.(994-996)aaG>aaT		cytosolic thiouridylase subunit 2 homolog (S. pombe)							64.0	66.0	66.0					16																	88779765		2189	4292	6481	SO:0001628	intergenic_variant	348180				tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding	g.chr16:88779765G>T	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		16.37:g.88779765G>T						CTU2_ENST00000453996.2_Missense_Mutation_p.K261N|CTU2_ENST00000312060.5_Missense_Mutation_p.K261N|CTU2_ENST00000378384.3_Missense_Mutation_p.K174N	p.K332N			Q2VPK5	CTU2_HUMAN			8	1005	+			261		V -> I (in dbSNP:rs4782321).			A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	c.996G>T	CCDS54058.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.623980	0.66901	.	.	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.18960	2.18;2.18;2.18	5.04	1.57	0.23409	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.43700	0.1259	M	0.83012	2.62	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.995;0.993;0.996	T	0.27971	-1.0058	10	0.46703	T	0.11	.	8.6687	0.34137	0.3454:0.0:0.6546:0.0	.	174;261;261	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	N	174;261;261	ENSP00000367635:K174N;ENSP00000308617:K261N;ENSP00000388320:K261N	ENSP00000308617:K261N	K	+	3	2	CTU2	87307266	0.991000	0.36638	1.000000	0.80357	0.941000	0.58515	0.624000	0.24462	0.398000	0.25338	0.655000	0.94253	AAG		0.657	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745		5	115	1	0	0.248553	1	0.256838	5	115				
ITPR3	3710	broad.mit.edu	37	6	33632679	33632679	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:33632679C>A	ENST00000374316.5	+	13	2241	c.1181C>A	c.(1180-1182)aCc>aAc	p.T394N	ITPR3_ENST00000605930.1_Missense_Mutation_p.T394N			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	394	MIR 5. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.T394N(4)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CACCTCTGCACCAACACGTGG	0.662																																						ENST00000374316.5																			4	Substitution - Missense(4)	p.T394N(4)	lung(4)	NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85						c.(1180-1182)aCc>aAc		inositol 1,4,5-trisphosphate receptor, type 3							62.0	57.0	59.0					6																	33632679		2203	4300	6503	SO:0001583	missense	3710				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding	g.chr6:33632679C>A	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1181C>A	6.37:g.33632679C>A	ENSP00000363435:p.Thr394Asn					ITPR3_ENST00000605930.1_Missense_Mutation_p.T394N	p.T394N			Q14573	ITPR3_HUMAN			13	2241	+			394			MIR 5.		Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	c.1181C>A	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305652	0.81247	.	.	ENSG00000096433	ENST00000374316	D	0.91124	-2.79	4.98	4.98	0.66077	MIR motif (2);MIR (2);	0.056367	0.64402	D	0.000001	D	0.95683	0.8596	M	0.88450	2.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	D	0.96464	0.9343	10	0.87932	D	0	-35.3408	17.8402	0.88713	0.0:1.0:0.0:0.0	.	394	Q14573	ITPR3_HUMAN	N	394	ENSP00000363435:T394N	ENSP00000363435:T394N	T	+	2	0	ITPR3	33740657	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	5.977000	0.70492	2.303000	0.77524	0.305000	0.20034	ACC		0.662	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		4	54	1	0	0.184627	1	0.19736	4	54				
RSPH3	83861	broad.mit.edu	37	6	159403544	159403544	+	Silent	SNP	C	C	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:159403544C>T	ENST00000252655.1	-	5	1284	c.1095G>A	c.(1093-1095)gaG>gaA	p.E365E	RSPH3_ENST00000367069.2_Silent_p.E223E|RSPH3_ENST00000297262.3_Silent_p.E269E|RSPH3_ENST00000449822.1_Silent_p.E127E	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	365										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		GCCTCTCTTGCTCTTCAAGTC	0.398																																						ENST00000367069.2																			0				endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23						c.(667-669)gaG>gaA		radial spoke 3 homolog (Chlamydomonas)							71.0	63.0	65.0					6																	159403544		2203	4300	6503	SO:0001819	synonymous_variant	83861							g.chr6:159403544C>T	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1095G>A	6.37:g.159403544C>T						RSPH3_ENST00000449822.1_Silent_p.E127E|RSPH3_ENST00000297262.3_Silent_p.E269E|RSPH3_ENST00000252655.1_Silent_p.E365E	p.E223E			Q86UC2	RSPH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)	5	1305	-		Breast(66;0.00519)|Ovarian(120;0.123)	365					Q96LQ5|Q96LX2|Q9BX75	Silent	SNP	ENST00000252655.1	37	c.669G>A	CCDS5260.1																																																																																				0.398	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		5	28	0	0	0	1	0	5	28				
SRP68	6730	broad.mit.edu	37	17	74068495	74068495	+	Silent	SNP	A	A	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:74068495A>C	ENST00000307877.2	-	1	239	c.78T>G	c.(76-78)ggT>ggG	p.G26G	SRP68_ENST00000355113.5_5'UTR|SRP68_ENST00000539137.1_Silent_p.G26G|GALR2_ENST00000329003.3_5'Flank	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	26					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						caccgccgctaccgccgccgc	0.657																																						ENST00000307877.2																			0				NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						c.(76-78)ggT>ggG		signal recognition particle 68kDa							16.0	23.0	21.0					17																	74068495		1866	3696	5562	SO:0001819	synonymous_variant	6730				response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding	g.chr17:74068495A>C	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.78T>G	17.37:g.74068495A>C						SRP68_ENST00000355113.5_5'UTR|SRP68_ENST00000539137.1_Silent_p.G26G	p.G26G	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN			1	239	-			26					B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Silent	SNP	ENST00000307877.2	37	c.78T>G	CCDS11738.1																																																																																				0.657	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		3	4	0	0	0	1	0	3	4				
PRPS1	5631	broad.mit.edu	37	X	106890921	106890921	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:106890921G>A	ENST00000372435.4	+	6	912	c.790G>A	c.(790-792)Gca>Aca	p.A264T	PRPS1_ENST00000543248.1_Missense_Mutation_p.A264T|PRPS1_ENST00000372418.1_Missense_Mutation_p.A164T|PRPS1_ENST00000372428.4_Missense_Mutation_p.A197T	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	264					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						CATCAACAACGCATGCTTTGA	0.453																																						ENST00000372435.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						c.(790-792)Gca>Aca		phosphoribosyl pyrophosphate synthetase 1							158.0	129.0	139.0					X																	106890921		2203	4300	6503	SO:0001583	missense	5631				5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity	g.chrX:106890921G>A	X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"""PRS I"", ""ribose-phosphate diphosphokinase 1"""	311850	"""deafness, X-linked 2, perceptive, congenital"""	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.790G>A	X.37:g.106890921G>A	ENSP00000361512:p.Ala264Thr					PRPS1_ENST00000372418.1_Missense_Mutation_p.A164T|PRPS1_ENST00000372428.4_Missense_Mutation_p.A197T|PRPS1_ENST00000543248.1_Missense_Mutation_p.A264T	p.A264T	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN			6	912	+			264					B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	37	c.790G>A	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.616749	0.66672	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000543248;ENST00000372418	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.67674	0.2918	M	0.63428	1.95	0.58432	D	0.999992	B;B	0.19935	0.04;0.04	B;B	0.13407	0.009;0.009	T	0.70339	-0.4899	10	0.62326	D	0.03	.	14.6655	0.68904	0.0:0.0:1.0:0.0	.	264;264	Q53FW2;P60891	.;PRPS1_HUMAN	T	264;197;264;164	ENSP00000361512:A264T;ENSP00000361505:A197T;ENSP00000443185:A264T;ENSP00000361495:A164T	ENSP00000361495:A164T	A	+	1	0	PRPS1	106777577	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	9.067000	0.93955	2.118000	0.64928	0.600000	0.82982	GCA		0.453	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1			10	109	0	0	0	1	0	10	109				
PIGZ	80235	broad.mit.edu	37	3	196674805	196674805	+	Silent	SNP	G	G	A	rs374868549		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr3:196674805G>A	ENST00000412723.1	-	3	1109	c.963C>T	c.(961-963)aaC>aaT	p.N321N		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	321					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		GCAGGAAGCCGTTGACTGCCA	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.001					ENST00000412723.1																			0				breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14						c.(961-963)aaC>aaT		phosphatidylinositol glycan anchor biosynthesis, class Z		G		1,4405	2.1+/-5.4	0,1,2202	98.0	105.0	102.0		963	-7.6	0.7	3		102	0,8600		0,0,4300	no	coding-synonymous	PIGZ	NM_025163.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		321/580	196674805	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	80235				GPI anchor biosynthetic process	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity	g.chr3:196674805G>A	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.963C>T	3.37:g.196674805G>A							p.N321N	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)	3	1109	-	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		321					Q9H9G6	Silent	SNP	ENST00000412723.1	37	c.963C>T	CCDS3324.1																																																																																				0.617	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		4	185	0	0	0	1	0	4	185				
TSSC2	650368	broad.mit.edu	37	11	3427765	3427765	+	RNA	SNP	G	G	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:3427765G>C	ENST00000529482.1	+	0	882									tumor suppressing subtransferable candidate 2 pseudogene																		CACACGTCCTGCAGTGGCCTG	0.602																																						ENST00000529482.1																			0																																																			0							g.chr11:3427765G>C			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427765G>C														0	882	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.602	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	62	0	0	0	1	0	4	62				
HIST1H2AL	8332	broad.mit.edu	37	6	27833429	27833429	+	Silent	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:27833429C>A	ENST00000357320.2	+	1	396	c.297C>A	c.(295-297)ggC>ggA	p.G99G		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	99						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						AGCTGCTGGGCAAAGTAACCA	0.592																																						ENST00000357320.2																			0				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						c.(295-297)ggC>ggA		histone cluster 1, H2al							129.0	124.0	125.0					6																	27833429		2203	4300	6503	SO:0001819	synonymous_variant	8332				nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding	g.chr6:27833429C>A	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.297C>A	6.37:g.27833429C>A							p.G99G	NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN			1	396	+			99					P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	c.297C>A	CCDS4634.1																																																																																				0.592	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511		5	194	1	0	8.12818e-05	1	9.33236e-05	5	194				
FAM129A	116496	broad.mit.edu	37	1	184863335	184863335	+	Silent	SNP	T	T	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr1:184863335T>C	ENST00000367511.3	-	3	385	c.192A>G	c.(190-192)ccA>ccG	p.P64P		NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	64					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CAGGCGCCAATGGTGGCTTAA	0.343																																						ENST00000367511.3																			0				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						c.(190-192)ccA>ccG		family with sequence similarity 129, member A							110.0	100.0	104.0					1																	184863335		2203	4300	6503	SO:0001819	synonymous_variant	116496				negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane		g.chr1:184863335T>C	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.192A>G	1.37:g.184863335T>C							p.P64P	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN			3	385	-			64					Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Silent	SNP	ENST00000367511.3	37	c.192A>G	CCDS1364.1																																																																																				0.343	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			5	54	0	0	0	1	0	5	54				
LRRC4C	57689	broad.mit.edu	37	11	40137057	40137057	+	Silent	SNP	G	G	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:40137057G>C	ENST00000278198.2	-	2	2749	c.786C>G	c.(784-786)gcC>gcG	p.A262A	LRRC4C_ENST00000530763.1_Silent_p.A262A|LRRC4C_ENST00000528697.1_Silent_p.A262A|LRRC4C_ENST00000527150.1_Silent_p.A262A			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	262					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				GGTTGTCAAAGGCATTCCGTT	0.453																																						ENST00000278198.2																			0				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86						c.(784-786)gcC>gcG		leucine rich repeat containing 4C							155.0	122.0	133.0					11																	40137057		2203	4300	6503	SO:0001819	synonymous_variant	57689				regulation of axonogenesis	integral to membrane	protein binding	g.chr11:40137057G>C	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.786C>G	11.37:g.40137057G>C						LRRC4C_ENST00000530763.1_Silent_p.A262A|LRRC4C_ENST00000528697.1_Silent_p.A262A|LRRC4C_ENST00000527150.1_Silent_p.A262A	p.A262A			Q9HCJ2	LRC4C_HUMAN			2	2749	-		all_lung(304;0.0575)|Lung NSC(402;0.138)	262					A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	c.786C>G	CCDS31464.1																																																																																				0.453	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		7	104	0	0	0	1	0	7	104				
ARAP3	64411	broad.mit.edu	37	5	141051740	141051740	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr5:141051740G>A	ENST00000239440.4	-	10	1579	c.1514C>T	c.(1513-1515)gCg>gTg	p.A505V	ARAP3_ENST00000513878.1_Missense_Mutation_p.A167V|ARAP3_ENST00000508305.1_Missense_Mutation_p.A427V	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	505	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CCCACAGTCCGCACACTGCCG	0.612																																						ENST00000239440.4																			0				NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						c.(1513-1515)gCg>gTg		ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3							137.0	136.0	136.0					5																	141051740		2203	4300	6503	SO:0001583	missense	64411				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding	g.chr5:141051740G>A	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1514C>T	5.37:g.141051740G>A	ENSP00000239440:p.Ala505Val					ARAP3_ENST00000508305.1_Missense_Mutation_p.A427V|ARAP3_ENST00000513878.1_Missense_Mutation_p.A167V	p.A505V	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN			10	1579	-			505			Arf-GAP.		B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	c.1514C>T	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.142199	0.77775	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.51071	0.72;0.72;0.72	3.51	3.51	0.40186	.	0.151693	0.41500	U	0.000870	T	0.63640	0.2528	L	0.59436	1.845	0.51012	D	0.999906	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.941;0.99	T	0.68633	-0.5357	10	0.87932	D	0	.	13.9666	0.64213	0.0:0.0:1.0:0.0	.	167;427;505	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	V	427;505;167	ENSP00000421826:A427V;ENSP00000239440:A505V;ENSP00000421468:A167V	ENSP00000239440:A505V	A	-	2	0	ARAP3	141031924	1.000000	0.71417	0.976000	0.42696	0.538000	0.34931	9.611000	0.98342	1.789000	0.52484	0.563000	0.77884	GCG		0.612	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		5	332	0	0	0	1	0	5	332				
FGF4	2249	broad.mit.edu	37	11	69588192	69588192	+	Missense_Mutation	SNP	T	T	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:69588192T>G	ENST00000168712.1	-	3	824	c.506A>C	c.(505-507)tAc>tCc	p.Y169S	FGF4_ENST00000538040.1_5'UTR|AP001888.1_ENST00000602104.1_5'Flank	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	169					apoptotic process involved in morphogenesis (GO:0060561)|cartilage condensation (GO:0001502)|cell-cell signaling (GO:0007267)|chondroblast differentiation (GO:0060591)|cranial suture morphogenesis (GO:0060363)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)	cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(3)	3	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)	GTAGGACTCGTAGGCGTTGTA	0.567																																						ENST00000168712.1																			0				lung(3)	3						c.(505-507)tAc>tCc		fibroblast growth factor 4	Pentosan Polysulfate(DB00686)						252.0	207.0	222.0					11																	69588192		2200	4294	6494	SO:0001583	missense	2249				cell-cell signaling|chondroblast differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade	extracellular region	growth factor activity|heparin binding	g.chr11:69588192T>G	M17446	CCDS8194.1	11q13.3	2014-01-30	2008-08-01		ENSG00000075388	ENSG00000075388		"""Endogenous ligands"""	3682	protein-coding gene	gene with protein product	"""human stomach cancer, transforming factor from FGF-related oncogene"", ""kaposi sarcoma oncogene"", ""transforming protein KS3"""	164980	"""heparin secretory transforming protein 1"""	HSTF1		1611909	Standard	NM_002007		Approved	K-FGF, HBGF-4, HST, HST-1, KFGF	uc001opg.1	P08620	OTTHUMG00000167887	ENST00000168712.1:c.506A>C	11.37:g.69588192T>G	ENSP00000168712:p.Tyr169Ser					FGF4_ENST00000538040.1_5'UTR	p.Y169S	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		3	824	-	Melanoma(5;1.89e-05)		169					B7U994	Missense_Mutation	SNP	ENST00000168712.1	37	c.506A>C	CCDS8194.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.981132	0.74474	.	.	ENSG00000075388	ENST00000168712	D	0.85258	-1.96	5.81	5.81	0.92471	.	0.000000	0.43260	D	0.000585	D	0.95510	0.8541	H	0.97918	4.105	0.80722	D	1	D	0.71674	0.998	D	0.91635	0.999	D	0.97228	0.9882	9	.	.	.	.	16.1612	0.81712	0.0:0.0:0.0:1.0	.	169	P08620	FGF4_HUMAN	S	169	ENSP00000168712:Y169S	.	Y	-	2	0	FGF4	69297373	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	7.337000	0.79256	2.216000	0.71823	0.533000	0.62120	TAC		0.567	FGF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396834.2	NM_002007		15	174	0	0	0	1	0	15	174				
PCSK5	5125	broad.mit.edu	37	9	78790192	78790192	+	Intron	SNP	C	C	G	rs200914896		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr9:78790192C>G	ENST00000545128.1	+	14	2438				PCSK5_ENST00000376767.3_Missense_Mutation_p.R683G|PCSK5_ENST00000376752.4_Intron	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ggaatggaatcgaatcgaatc	0.373																																						ENST00000376767.3																			0				NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						c.(2047-2049)Cga>Gga		proprotein convertase subtilisin/kexin type 5																																				SO:0001627	intron_variant	5125				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity	g.chr9:78790192C>G		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1900+147C>G	9.37:g.78790192C>G						PCSK5_ENST00000545128.1_Intron|PCSK5_ENST00000376752.4_Intron	p.R683G			Q92824	PCSK5_HUMAN			14	2559	+			0			CRM (Cys-rich motif).		F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	c.2047C>G	CCDS55320.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	0.525|0.525	-0.860634|-0.860634	0.02610|0.02610	.|.	.|.	ENSG00000099139|ENSG00000099139	ENST00000376767|ENST00000396108	T|.	0.65916|.	-0.18|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35098|0.35098	0.0920|0.0920	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.38045|0.38045	-0.9679|-0.9679	7|4	0.07325|0.87932	T|D	0.83|0	.|.	2.8186|2.8186	0.05465|0.05465	0.5:0.5:0.0:0.0|0.5:0.5:0.0:0.0	.|.	683|.	B1AMG5|.	.|.	G|W	683|681	ENSP00000365958:R683G|.	ENSP00000365958:R683G|ENSP00000379415:S681W	R|S	+|+	1|2	2|0	PCSK5|PCSK5	77980012|77980012	0.000000|0.000000	0.05858|0.05858	0.075000|0.075000	0.20258|0.20258	0.077000|0.077000	0.17291|0.17291	-2.681000|-2.681000	0.00837|0.00837	-0.000000|-0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	CGA|TCG		0.373	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				3	5	0	0	0	1	0	3	5				
MROH2B	133558	broad.mit.edu	37	5	41065560	41065560	+	Silent	SNP	C	C	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr5:41065560C>T	ENST00000399564.4	-	4	684	c.234G>A	c.(232-234)gaG>gaA	p.E78E		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	78																	ACACCAAAACCTCACCAGCTA	0.413																																						ENST00000399564.4																			0											c.(232-234)gaG>gaA		maestro heat-like repeat family member 2B							93.0	86.0	88.0					5																	41065560		1911	4117	6028	SO:0001819	synonymous_variant	133558							g.chr5:41065560C>T		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.234G>A	5.37:g.41065560C>T							p.E78E	NM_173489.4	NP_775760.3					4	684	-								Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	c.234G>A	CCDS47202.1																																																																																				0.413	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		3	44	0	0	0	1	0	3	44				
BMS1P20	96610	broad.mit.edu	37	22	22664141	22664141	+	RNA	SNP	G	G	A	rs369590722		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr22:22664141G>A	ENST00000426066.1	+	0	664					NR_027293.1				BMS1 pseudogene 20																		AAATTTGAAGGTGCTGTGATT	0.448																																						ENST00000426066.1																			0																																																			0							g.chr22:22664141G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664141G>A								NR_027293.1						0	664	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.448	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			5	74	0	0	0	1	0	5	74				
DNAH9	1770	broad.mit.edu	37	17	11835360	11835360	+	Silent	SNP	G	G	A	rs374717515		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:11835360G>A	ENST00000262442.4	+	64	12203	c.12135G>A	c.(12133-12135)acG>acA	p.T4045T	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Silent_p.T357T|DNAH9_ENST00000454412.2_Silent_p.T3969T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4045	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTCGGGAGACGGAGTTTAAGA	0.493																																						ENST00000262442.3																			0				NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290						c.(12133-12135)acG>acA		dynein, axonemal, heavy chain 9		G	,	0,4406		0,0,2203	342.0	317.0	325.0		12135,1071	-9.9	0.0	17		325	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DNAH9	NM_001372.3,NM_004662.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	4045/4487,357/799	11835360	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1770				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:11835360G>A	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.12135G>A	17.37:g.11835360G>A						DNAH9_ENST00000396001.2_Silent_p.T357T|DNAH9_ENST00000454412.2_Silent_p.T3969T	p.T4045T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	64	12203	+		Breast(5;0.0122)|all_epithelial(5;0.131)	4045			AAA 6 (By similarity).		A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	c.12135G>A	CCDS11160.1																																																																																				0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		6	332	0	0	0	1	0	6	332				
KIAA0100	9703	broad.mit.edu	37	17	26961608	26961608	+	Silent	SNP	A	A	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:26961608A>G	ENST00000528896.2	-	16	3071	c.2997T>C	c.(2995-2997)ccT>ccC	p.P999P	KIAA0100_ENST00000389003.3_Silent_p.P856P|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000544884.1_Silent_p.P856P|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	999						extracellular region (GO:0005576)		p.P999P(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CAGGGGGAAAAGGGCTGCCTG	0.493																																						ENST00000528896.2																			1	Substitution - coding silent(1)	p.P999P(1)	prostate(1)	breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68						c.(2995-2997)ccT>ccC		KIAA0100							110.0	106.0	107.0					17																	26961608		2203	4300	6503	SO:0001819	synonymous_variant	9703					extracellular region		g.chr17:26961608A>G	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2997T>C	17.37:g.26961608A>G						KIAA0100_ENST00000389003.3_Silent_p.P856P|RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Silent_p.P856P	p.P999P	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN			16	3071	-	Lung NSC(42;0.00431)		999					A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Silent	SNP	ENST00000528896.2	37	c.2997T>C	CCDS32595.1																																																																																				0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		4	150	0	0	0	1	0	4	150				
CCDC22	28952	broad.mit.edu	37	X	49093732	49093732	+	Splice_Site	SNP	T	T	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:49093732T>G	ENST00000376227.3	+	2	398		c.e2+2		CCDC22_ENST00000496651.1_Splice_Site	NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22											NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						GCCTGCATGGTGAGTGGCCCT	0.562																																						ENST00000376227.3																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						c.e2+2		coiled-coil domain containing 22							65.0	49.0	55.0					X																	49093732		2203	4300	6503	SO:0001630	splice_region_variant	28952							g.chrX:49093732T>G	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.228+2T>G	X.37:g.49093732T>G						CCDC22_ENST00000496651.1_Splice_Site		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN			2	398	+								A8K7G1	Splice_Site	SNP	ENST00000376227.3	37		CCDS14322.1	.	.	.	.	.	.	.	.	.	.	t	20.8	4.048787	0.75846	.	.	ENSG00000101997	ENST00000376227;ENST00000538876	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4494	0.61161	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC22	48980676	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.007000	0.76335	1.819000	0.53055	0.347000	0.21830	.		0.562	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	Intron	5	88	0	0	0	1	0	5	88				
CCDC173	129881	broad.mit.edu	37	2	170518798	170518798	+	Silent	SNP	G	G	T	rs200900002		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr2:170518798G>T	ENST00000447353.1	-	5	916	c.811C>A	c.(811-813)Cgg>Agg	p.R271R		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	271																	ACAAGAAACCGTCTCCTGCTT	0.313																																						ENST00000447353.1																			0											c.(811-813)Cgg>Agg		coiled-coil domain containing 173							235.0	228.0	230.0					2																	170518798		1816	4074	5890	SO:0001819	synonymous_variant	129881							g.chr2:170518798G>T	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.811C>A	2.37:g.170518798G>T							p.R271R	NM_001085447.1	NP_001078916.1					5	916	-								Q6PJF6	Silent	SNP	ENST00000447353.1	37	c.811C>A	CCDS46445.1																																																																																				0.313	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		5	145	1	0	0.0293803	1	0.0325282	5	145				
IDH2	3418	broad.mit.edu	37	15	90631839	90631839	+	Missense_Mutation	SNP	T	T	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr15:90631839T>A	ENST00000330062.3	-	4	627	c.514A>T	c.(514-516)Agg>Tgg	p.R172W	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R120W|IDH2_ENST00000539790.1_Missense_Mutation_p.R42W	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172W(12)|p.R172G(2)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			TGGGCGTGCCTGCCAATGGTG	0.627			M		GBM																																	ENST00000330062.3				Dom	yes		15	15q26.1	3418	M	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """			M			GBM		14	Substitution - Missense(14)	p.R172W(12)|p.R172G(2)	central_nervous_system(9)|biliary_tract(5)	biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109						c.(514-516)Agg>Tgg		isocitrate dehydrogenase 2 (NADP+), mitochondrial							86.0	81.0	83.0					15																	90631839		2200	4298	6498	SO:0001583	missense	3418				2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding	g.chr15:90631839T>A		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.514A>T	15.37:g.90631839T>A	ENSP00000331897:p.Arg172Trp					IDH2_ENST00000540499.2_Missense_Mutation_p.R120W|IDH2_ENST00000539790.1_Missense_Mutation_p.R42W|IDH2_ENST00000559482.1_Intron	p.R172W	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)		4	627	-	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		172					B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	c.514A>T	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495142	0.44352	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.87029	-2.2;-2.2;-2.2	5.93	0.717	0.18196	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	H	0.98487	4.245	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.95508	0.8583	10	0.87932	D	0	.	13.7144	0.62687	0.0:0.0:0.4915:0.5085	.	172	P48735	IDHP_HUMAN	W	172;42;120	ENSP00000331897:R172W;ENSP00000438457:R42W;ENSP00000446147:R120W	ENSP00000331897:R172W	R	-	1	2	IDH2	88432843	1.000000	0.71417	0.032000	0.17829	0.002000	0.02628	1.525000	0.35953	-0.113000	0.11958	-0.466000	0.05196	AGG		0.627	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			8	80	0	0	0	1	0	8	80				
NHEJ1	79840	broad.mit.edu	37	2	220012390	220012390	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr2:220012390G>A	ENST00000356853.5	-	4	651	c.518C>T	c.(517-519)aCg>aTg	p.T173M	NHEJ1_ENST00000409720.1_Missense_Mutation_p.T173M	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	173					B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TCGAATCAGCGTAGCCCCACT	0.478								Non-homologous end-joining																														ENST00000356853.5																			0				kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12						c.(517-519)aCg>aTg	Non-homologous end-joining	nonhomologous end-joining factor 1							168.0	132.0	144.0					2																	220012390		2203	4300	6503	SO:0001583	missense	79840				B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding	g.chr2:220012390G>A	AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736			25737	protein-coding gene	gene with protein product		611290				16439204, 16439205	Standard	NM_024782		Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.518C>T	2.37:g.220012390G>A	ENSP00000349313:p.Thr173Met					NHEJ1_ENST00000409720.1_Missense_Mutation_p.T173M	p.T173M	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)	4	651	-		Renal(207;0.0915)	173					B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	Missense_Mutation	SNP	ENST00000356853.5	37	c.518C>T	CCDS2432.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941432	0.34283	.	.	ENSG00000187736	ENST00000409720;ENST00000356853;ENST00000426304;ENST00000457600	T;T;T;T	0.65916	0.19;0.23;0.36;-0.18	5.71	-2.33	0.06724	.	1.169160	0.06511	U	0.738065	T	0.51568	0.1682	L	0.43152	1.355	0.09310	N	1	B	0.33528	0.416	B	0.28784	0.094	T	0.46317	-0.9200	10	0.46703	T	0.11	-0.014	12.2305	0.54484	0.6337:0.0:0.3663:0.0	.	173	Q9H9Q4	NHEJ1_HUMAN	M	173;173;93;173	ENSP00000387290:T173M;ENSP00000349313:T173M;ENSP00000394896:T93M;ENSP00000407201:T173M	ENSP00000349313:T173M	T	-	2	0	NHEJ1	219720634	0.000000	0.05858	0.010000	0.14722	0.971000	0.66376	0.153000	0.16323	-0.255000	0.09486	0.650000	0.86243	ACG		0.478	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256817.2	NM_024782		4	54	0	0	0	1	0	4	54				
FREM1	158326	broad.mit.edu	37	9	14845980	14845980	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr9:14845980C>A	ENST00000380880.3	-	8	2154	c.1371G>T	c.(1369-1371)caG>caT	p.Q457H	FREM1_ENST00000422223.2_Missense_Mutation_p.Q457H|FREM1_ENST00000380881.4_Missense_Mutation_p.Q458H			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	457					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GCCATCCATGCTGCAGGCCAC	0.443																																						ENST00000380881.4																			0				breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100						c.(1372-1374)caG>caT		FRAS1 related extracellular matrix 1							57.0	61.0	60.0					9																	14845980		2089	4238	6327	SO:0001583	missense	158326				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding	g.chr9:14845980C>A	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1371G>T	9.37:g.14845980C>A	ENSP00000370262:p.Gln457His					FREM1_ENST00000380880.3_Missense_Mutation_p.Q457H|FREM1_ENST00000422223.2_Missense_Mutation_p.Q457H	p.Q458H			Q5H8C1	FREM1_HUMAN		GBM - Glioblastoma multiforme(50;3.53e-06)	9	2189	-			457					B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	c.1374G>T	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472423	0.43942	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.27104	1.69;1.69;1.69	4.91	0.196	0.15159	.	0.280340	0.41396	N	0.000882	T	0.34077	0.0885	M	0.76574	2.34	0.40849	D	0.983739	P	0.52692	0.955	P	0.54924	0.764	T	0.10314	-1.0635	10	0.45353	T	0.12	-0.7808	3.4819	0.07605	0.2748:0.3579:0.0:0.3673	.	457	Q5H8C1	FREM1_HUMAN	H	458;457;457	ENSP00000370263:Q458H;ENSP00000412940:Q457H;ENSP00000370262:Q457H	ENSP00000370257:Q460H	Q	-	3	2	FREM1	14835980	0.986000	0.35501	0.957000	0.39632	0.478000	0.33099	0.276000	0.18716	-0.178000	0.10672	0.462000	0.41574	CAG		0.443	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		3	27	1	0	1	1	1	3	27				
GAB2	9846	broad.mit.edu	37	11	77934697	77934697	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:77934697G>A	ENST00000361507.4	-	6	1413	c.1328C>T	c.(1327-1329)tCg>tTg	p.S443L	GAB2_ENST00000340149.2_Missense_Mutation_p.S405L	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	443					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GGTGCTGTCCGATCGGCCCAC	0.478																																						ENST00000361507.4																		INTS4/GAB2(2)	0				NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24						c.(1327-1329)tCg>tTg		GRB2-associated binding protein 2							224.0	229.0	228.0					11																	77934697		2200	4292	6492	SO:0001583	missense	9846				osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity	g.chr11:77934697G>A	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1328C>T	11.37:g.77934697G>A	ENSP00000354952:p.Ser443Leu					GAB2_ENST00000340149.2_Missense_Mutation_p.S405L	p.S443L	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)		6	1413	-	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		443					A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	37	c.1328C>T	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.149748	0.37923	.	.	ENSG00000033327	ENST00000340149;ENST00000361507	T;T	0.18657	2.2;2.2	4.97	4.06	0.47325	.	0.175418	0.39210	U	0.001426	T	0.19565	0.0470	L	0.54323	1.7	0.54753	D	0.999987	B	0.17268	0.021	B	0.06405	0.002	T	0.04593	-1.0940	10	0.13470	T	0.59	-9.1923	13.3925	0.60832	0.075:0.0:0.925:0.0	.	443	Q9UQC2	GAB2_HUMAN	L	405;443	ENSP00000343959:S405L;ENSP00000354952:S443L	ENSP00000343959:S405L	S	-	2	0	GAB2	77612345	1.000000	0.71417	0.095000	0.20976	0.480000	0.33159	7.402000	0.79972	1.331000	0.45412	0.561000	0.74099	TCG		0.478	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		6	316	0	0	0	1	0	6	316				
HLA-A	3105	broad.mit.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376802.2_Silent_p.V49V|HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_Silent_p.V49V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	49	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.V49V(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCATCGCCGTGGGCTACGTGG	0.692									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																												ENST00000396634.1																			2	Substitution - coding silent(2)	p.V49V(2)	lung(1)|kidney(1)	central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						c.(145-147)gtG>gtC		major histocompatibility complex, class I, A																																				SO:0001819	synonymous_variant	3105	Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity	g.chr6:29910607G>C	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.147G>C	6.37:g.29910607G>C		Multiple Myeloma(9;0.094)				HLA-A_ENST00000376802.2_Silent_p.V49V|HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_Silent_p.V49V	p.V49V			P30443	1A01_HUMAN			4	488	+			49			Alpha-1.		O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	c.147G>C	CCDS34373.1																																																																																				0.692	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		4	68	0	0	0	1	0	4	68				
RYR2	6262	broad.mit.edu	37	1	237954771	237954771	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr1:237954771delT	ENST00000366574.2	+	93	13836	c.13519delT	c.(13519-13521)ttafs	p.L4507fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.L4513fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.L4491fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4507					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AATGTTAGCCTTATTTGTCGC	0.343																																						ENST00000366574.2																			0				NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586						c.(13519-13521)tafs		ryanodine receptor 2 (cardiac)							206.0	180.0	188.0					1																	237954771		1847	4091	5938	SO:0001589	frameshift_variant	6262				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding	g.chr1:237954771delT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13519delT	1.37:g.237954771delT	ENSP00000355533:p.Leu4507fs					RYR2_ENST00000542537.1_Frame_Shift_Del_p.L4491fs|RYR2_ENST00000360064.6_Frame_Shift_Del_p.L4513fs	p.L4507fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		93	13836	+	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	4507					Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	37	c.13519delT	CCDS55691.1																																																																																				0.343	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		2	4						2	4	---	---	---	---
NUTM2B-AS1	101060691	broad.mit.edu	37	10	81444708	81444708	+	RNA	DEL	G	G	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr10:81444708delG	ENST00000600376.1	-	0	54				RP11-119F19.2_ENST00000596088.1_RNA																							AGCAGTGCAAGGTCCACGTGC	0.577																																						ENST00000600376.1																			0																																																			0							g.chr10:81444708delG																													10.37:g.81444708delG						RP11-119F19.2_ENST00000596088.1_RNA								0	54	-									RNA	DEL	ENST00000600376.1	37																																																																																						0.577	RP11-119F19.2-004	KNOWN	basic	antisense	antisense	OTTHUMT00000461766.1			2	4						2	4	---	---	---	---
RP13-329D4.3	0	broad.mit.edu	37	20	26113543	26113543	+	lincRNA	DEL	A	A	-	rs375245697		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr20:26113543delA	ENST00000416563.1	-	0	250																											TCTTTGCCTTAACAACATTAT	0.363																																						ENST00000416563.1																			0																																																			0							g.chr20:26113543delA																													20.37:g.26113543delA														0	250	-									RNA	DEL	ENST00000416563.1	37																																																																																						0.363	RP13-329D4.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000078482.1			2	4						2	4	---	---	---	---
CD99L2	83692	broad.mit.edu	37	X	149984524	149984526	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:149984524_149984526delGTG	ENST00000370377.3	-	3	273_275	c.156_158delCAC	c.(154-159)accaca>aca	p.52_53TT>T	CD99L2_ENST00000466436.1_Intron|CD99L2_ENST00000346693.4_5'UTR|CD99L2_ENST00000437787.2_In_Frame_Del_p.52_53TT>T|CD99L2_ENST00000355149.3_Intron	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	52	Poly-Thr.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CCTATTGGTTGTGGTGGTGGTGG	0.552																																						ENST00000370377.3																			0				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23						c.(154-159)aca>ac		CD99 molecule-like 2																																				SO:0001651	inframe_deletion	83692				cell adhesion	cell junction|integral to membrane		g.chrX:149984524_149984526delGTG	BC030536	CCDS14697.1, CCDS14698.1, CCDS35427.1, CCDS55527.1, CCDS76044.1	Xq28	2007-12-04	2006-03-28	2003-02-14	ENSG00000102181	ENSG00000102181			18237	protein-coding gene	gene with protein product		300846	"""MIC2 like 1"", ""CD99 antigen-like 2"""	MIC2L1			Standard	NM_001184808		Approved	CD99B	uc004fek.3	Q8TCZ2	OTTHUMG00000024247	ENST00000370377.3:c.156_158delCAC	X.37:g.149984533_149984535delGTG	ENSP00000359403:p.Thr54del					CD99L2_ENST00000466436.1_Intron|CD99L2_ENST00000355149.3_Intron|CD99L2_ENST00000437787.2_In_Frame_Del_p.TT52del|CD99L2_ENST00000346693.4_5'UTR	p.TT52del	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN			3	273_275	-	Acute lymphoblastic leukemia(192;6.56e-05)		52			Poly-Thr.		A8K2D5|A8K5R0|B3KWG2|B4DDL7|E7EMK5|E9PD27|Q8TAW2|Q8TCZ0|Q8TCZ1|Q9BQG9	In_Frame_Del	DEL	ENST00000370377.3	37	c.156_158delCAC	CCDS35427.1																																																																																				0.552	CD99L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061199.1	NM_031462		7	347						7	347	---	---	---	---
