#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
AHNAK2	113146	broad.mit.edu	37	14	105413382	105413382	+	Silent	SNP	G	G	A	rs374049138		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr14:105413382G>A	ENST00000333244.5	-	7	8525	c.8406C>T	c.(8404-8406)gcC>gcT	p.A2802A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2802						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCCCTTGTCGGCCAGGGACA	0.617																																						ENST00000333244.5																			0				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33						c.(8404-8406)gcC>gcT		AHNAK nucleoprotein 2		G		0,3888		0,0,1944	199.0	214.0	209.0		8406	-6.5	0.0	14		209	1,8267		0,1,4133	no	coding-synonymous	AHNAK2	NM_138420.2		0,1,6077	AA,AG,GG		0.0121,0.0,0.0082		2802/5796	105413382	1,12155	1944	4134	6078	SO:0001819	synonymous_variant	113146					nucleus		g.chr14:105413382G>A	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8406C>T	14.37:g.105413382G>A						AHNAK2_ENST00000557457.1_Intron	p.A2802A	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		7	8525	-		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	2802					Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	c.8406C>T	CCDS45177.1																																																																																				0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		6	477	0	0	0	1	0	6	477				
POTEF	728378	broad.mit.edu	37	2	130877845	130877845	+	Missense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:130877845C>T	ENST00000409914.2	-	3	643	c.244G>A	c.(244-246)Gct>Act	p.A82T	POTEF_ENST00000361163.4_Missense_Mutation_p.A82T|POTEF_ENST00000357462.5_Missense_Mutation_p.A82T|POTEF_ENST00000360967.5_Missense_Mutation_p.A82T	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	82					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TCTCCAGAAGCGCCCACGTTG	0.602																																						ENST00000357462.5																			0				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						c.(244-246)Gct>Act		POTE ankyrin domain family, member F							92.0	123.0	113.0					2																	130877845		2202	4294	6496	SO:0001583	missense	728378					cell cortex	ATP binding	g.chr2:130877845C>T	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.244G>A	2.37:g.130877845C>T	ENSP00000386786:p.Ala82Thr					POTEF_ENST00000360967.5_Missense_Mutation_p.A82T|POTEF_ENST00000361163.4_Missense_Mutation_p.A82T|POTEF_ENST00000409914.2_Missense_Mutation_p.A82T	p.A82T			A5A3E0	POTEF_HUMAN			1	337	-			82					A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	c.244G>A	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.989305	0.00439	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.75260	-0.92;-0.92;1.92;1.91	0.586	0.586	0.17434	.	.	.	.	.	T	0.32041	0.0816	N	0.01505	-0.83	0.09310	N	1	P	0.52463	0.953	B	0.32149	0.141	T	0.45011	-0.9290	8	0.02654	T	1	.	.	.	.	.	82	A5A3E0	POTEF_HUMAN	T	82	ENSP00000350052:A82T;ENSP00000386786:A82T;ENSP00000354232:A82T;ENSP00000355012:A82T	ENSP00000350052:A82T	A	-	1	0	POTEF	130594315	0.000000	0.05858	0.002000	0.10522	0.090000	0.18270	-0.188000	0.09642	0.590000	0.29694	0.152000	0.16155	GCT		0.602	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		5	388	0	0	0	1	0	5	388				
SMPD4	55627	broad.mit.edu	37	2	130930857	130930857	+	Silent	SNP	A	A	G	rs557431954	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:130930857A>G	ENST00000409031.1	-	5	1605	c.457T>C	c.(457-459)Ttg>Ctg	p.L153L	SMPD4_ENST00000339679.7_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000351288.6_Silent_p.L153L|SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000431183.2_Intron	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	114					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CTTACAGGCAAGTAGGAGACA	0.488													.|||	4	0.000798722	0.0	0.0	5008	,	,		20338	0.0		0.004	False		,,,				2504	0.0					ENST00000409031.1																			0				breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(457-459)Ttg>Ctg		sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	Phosphatidylserine(DB00144)						120.0	118.0	119.0					2																	130930857		2203	4300	6503	SO:0001819	synonymous_variant	55627				sphingomyelin catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|trans-Golgi network	metal ion binding|protein binding|sphingomyelin phosphodiesterase activity|sphingomyelin phosphodiesterase D activity	g.chr2:130930857A>G	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.457T>C	2.37:g.130930857A>G						SMPD4_ENST00000339679.7_Intron|SMPD4_ENST00000351288.6_Silent_p.L153L|SMPD4_ENST00000431183.2_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000426662.2_Intron	p.L153L	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN			5	1605	-	Colorectal(110;0.1)		114					B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Silent	SNP	ENST00000409031.1	37	c.457T>C	CCDS42751.1																																																																																				0.488	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		4	116	0	0	0	1	0	4	116				
IMMP1L	196294	broad.mit.edu	37	11	31477878	31477878	+	Silent	SNP	T	T	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr11:31477878T>G	ENST00000278200.1	-	5	445	c.250A>C	c.(250-252)Aga>Cga	p.R84R	IMMP1L_ENST00000528161.1_5'UTR|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000532287.1_Silent_p.R84R	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	84					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					CCAATTACTCTTTTACAAATA	0.318																																						ENST00000278200.1																			0				breast(1)|cervix(1)|large_intestine(1)|lung(4)	7						c.(250-252)Aga>Cga		IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)							64.0	59.0	61.0					11																	31477878		2202	4296	6498	SO:0001819	synonymous_variant	196294				proteolysis	mitochondrial inner membrane	serine-type peptidase activity	g.chr11:31477878T>G		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.250A>C	11.37:g.31477878T>G						IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000528161.1_5'UTR|IMMP1L_ENST00000532287.1_Silent_p.R84R	p.R84R	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN			5	445	-	Lung SC(675;0.225)		84					D3DQZ7|Q96SH9	Silent	SNP	ENST00000278200.1	37	c.250A>C	CCDS7874.1																																																																																				0.318	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		7	50	0	0	0	1	0	7	50				
RPTN	126638	broad.mit.edu	37	1	152128186	152128186	+	Silent	SNP	A	A	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr1:152128186A>G	ENST00000316073.3	-	3	1453	c.1389T>C	c.(1387-1389)taT>taC	p.Y463Y		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	463	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CTGTCTGACCATAGTGGGAAC	0.512																																						ENST00000316073.3																			0				breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						c.(1387-1389)taT>taC		repetin							788.0	697.0	725.0					1																	152128186		1568	3582	5150	SO:0001819	synonymous_variant	126638					proteinaceous extracellular matrix	calcium ion binding	g.chr1:152128186A>G	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1389T>C	1.37:g.152128186A>G							p.Y463Y	NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN			3	1453	-			463			Gln-rich.		B7ZBZ3	Silent	SNP	ENST00000316073.3	37	c.1389T>C	CCDS41397.1																																																																																				0.512	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		9	973	0	0	0	1	0	9	973				
SDHAP3	728609	broad.mit.edu	37	5	1593264	1593264	+	lincRNA	SNP	C	C	T	rs111700178		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:1593264C>T	ENST00000605200.1	+	0	0				SDHAP3_ENST00000436493.2_RNA																							AGGGCACATGCCTGACCAAAG	0.557																																						ENST00000436493.2																			0																																																			728609							g.chr5:1593264C>T																													5.37:g.1593264C>T														0	361	-									RNA	SNP	ENST00000605200.1	37																																																																																						0.557	CTD-2012J19.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000469651.1			5	46	0	0	0	1	0	5	46				
WFDC9	259240	broad.mit.edu	37	20	44236772	44236772	+	Missense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:44236772G>A	ENST00000326000.1	-	5	464	c.247C>T	c.(247-249)Ctt>Ttt	p.L83F		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	83						extracellular region (GO:0005576)				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				ATTGATTTAAGGGGCTCTCTA	0.423																																						ENST00000326000.1																			0				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6						c.(247-249)Ctt>Ttt		WAP four-disulfide core domain 9							178.0	180.0	180.0					20																	44236772		2203	4300	6503	SO:0001583	missense	259240					extracellular region		g.chr20:44236772G>A	AL031671	CCDS13362.1	20q13.12	2013-01-21			ENSG00000180205	ENSG00000180205		"""WAP four-disulfide core domain containing"""	20380	protein-coding gene	gene with protein product						12206714	Standard	NM_147198		Approved	WAP9, dJ688G8.2	uc002xoy.3	Q8NEX5	OTTHUMG00000046332	ENST00000326000.1:c.247C>T	20.37:g.44236772G>A	ENSP00000320532:p.Leu83Phe						p.L83F	NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN			5	464	-		Myeloproliferative disorder(115;0.0122)	83					Q3MIX6|Q5TGZ8	Missense_Mutation	SNP	ENST00000326000.1	37	c.247C>T	CCDS13362.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.670890	0.00758	.	.	ENSG00000180205	ENST00000326000	T	0.33865	1.39	3.62	1.08	0.20341	.	0.599477	0.13978	N	0.349644	T	0.13798	0.0334	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27872	-1.0061	9	0.09084	T	0.74	-2.5934	2.9681	0.05913	0.6667:0.0:0.1208:0.2125	.	83	Q8NEX5	WFDC9_HUMAN	F	83	ENSP00000320532:L83F	ENSP00000320532:L83F	L	-	1	0	WFDC9	43670186	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.388000	0.20735	0.238000	0.21222	-0.441000	0.05720	CTT		0.423	WFDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106945.1			4	185	0	0	0	1	0	4	185				
FNDC3A	22862	broad.mit.edu	37	13	49765404	49765404	+	Missense_Mutation	SNP	A	A	G	rs373752125		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr13:49765404A>G	ENST00000492622.2	+	19	2415	c.2110A>G	c.(2110-2112)Ata>Gta	p.I704V	FNDC3A_ENST00000541916.1_Missense_Mutation_p.I704V|FNDC3A_ENST00000398316.3_Missense_Mutation_p.I648V	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	704	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		AATGTCTCCTATAGAAAAAGA	0.413																																						ENST00000492622.2																			0				endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41						c.(2110-2112)Ata>Gta		fibronectin type III domain containing 3A		A	VAL/ILE,VAL/ILE	0,4406		0,0,2203	101.0	101.0	101.0		1942,2110	-2.8	1.0	13		101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FNDC3A	NM_014923.3,NM_001079673.1	29,29	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	648/1143,704/1199	49765404	1,13005	2203	4300	6503	SO:0001583	missense	22862					Golgi membrane|integral to membrane		g.chr13:49765404A>G	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.2110A>G	13.37:g.49765404A>G	ENSP00000417257:p.Ile704Val					FNDC3A_ENST00000398316.3_Missense_Mutation_p.I648V|FNDC3A_ENST00000541916.1_Missense_Mutation_p.I704V	p.I704V	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)	19	2415	+		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	704			Fibronectin type-III 5.		B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	c.2110A>G	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	A	8.158	0.788829	0.16258	0.0	1.16E-4	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.55234	0.53;0.53;0.53	5.2	-2.83	0.05769	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.173980	0.06240	N	0.690202	T	0.20373	0.0490	N	0.02315	-0.6	0.21579	N	0.99963	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09037	-1.0693	10	0.29301	T	0.29	-4.0E-4	0.4799	0.00546	0.3414:0.1995:0.2568:0.2023	.	648;704	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	V	704;640;704;648	ENSP00000417257:I704V;ENSP00000441831:I704V;ENSP00000381362:I648V	ENSP00000338579:I640V	I	+	1	0	FNDC3A	48663405	0.000000	0.05858	0.988000	0.46212	0.872000	0.50106	-0.689000	0.05144	-0.311000	0.08754	-0.366000	0.07423	ATA		0.413	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		12	81	0	0	0	1	0	12	81				
CD97	976	broad.mit.edu	37	19	14507920	14507920	+	Silent	SNP	G	G	A	rs148941728	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr19:14507920G>A	ENST00000242786.5	+	6	590	c.510G>A	c.(508-510)ccG>ccA	p.P170P	CD97_ENST00000358600.3_Intron|CD97_ENST00000587728.1_Intron|CD97_ENST00000357355.3_Intron	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	170	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GACAAAACCCGTGCCACAGCT	0.627													G|||	2	0.000399361	0.0	0.0	5008	,	,		16814	0.0		0.002	False		,,,				2504	0.0					ENST00000242786.5																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						c.(508-510)ccG>ccA		CD97 molecule		G	,,	1,4405	2.1+/-5.4	0,1,2202	108.0	97.0	101.0		,,510	-7.1	0.0	19	dbSNP_134	101	0,8600		0,0,4300	no	intron,intron,coding-synonymous	CD97	NM_001025160.2,NM_001784.4,NM_078481.3	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	,,170/836	14507920	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	976				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding	g.chr19:14507920G>A		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.510G>A	19.37:g.14507920G>A						CD97_ENST00000587728.1_Intron|CD97_ENST00000358600.3_Intron|CD97_ENST00000357355.3_Intron	p.P170P	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN			6	590	+			170			EGF-like 4; calcium-binding (Potential).		A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	37	c.510G>A	CCDS32929.1																																																																																				0.627	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		4	108	0	0	0	1	0	4	108				
ROS1	6098	broad.mit.edu	37	6	117662679	117662679	+	Missense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:117662679C>T	ENST00000368508.3	-	29	4984	c.4786G>A	c.(4786-4788)Gca>Aca	p.A1596T	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.A1590T	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1596	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TGTGAGATTGCCAACTGATAA	0.438			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3				Dom	yes		6	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)			"""O, E"""	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""		"""glioblastoma, NSCLC"""	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	0				NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162						c.(4786-4788)Gca>Aca		c-ros oncogene 1 , receptor tyrosine kinase							192.0	171.0	178.0					6																	117662679		2203	4300	6503	SO:0001583	missense	6098				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117662679C>T	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4786G>A	6.37:g.117662679C>T	ENSP00000357494:p.Ala1596Thr					ROS1_ENST00000368507.3_Missense_Mutation_p.A1590T|GOPC_ENST00000467125.1_Intron	p.A1596T	NM_002944.2	NP_002935.2	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	29	4984	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	1596			Fibronectin type-III 7.		Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	c.4786G>A	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	2.801	-0.249071	0.05867	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.52526	0.66;0.66	5.11	4.23	0.50019	.	0.432597	0.21624	N	0.071589	T	0.14743	0.0356	N	0.24115	0.695	0.52501	D	0.999958	P	0.34522	0.455	B	0.27608	0.081	T	0.05022	-1.0911	10	0.22109	T	0.4	.	9.8939	0.41306	0.0:0.9019:0.0:0.0981	.	1596	P08922	ROS1_HUMAN	T	1596;1590	ENSP00000357494:A1596T;ENSP00000357493:A1590T	ENSP00000357493:A1590T	A	-	1	0	ROS1	117769372	0.003000	0.15002	0.769000	0.31535	0.697000	0.40408	0.040000	0.13905	2.390000	0.81377	0.655000	0.94253	GCA		0.438	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			4	95	0	0	0	1	0	4	95				
GPCPD1	56261	broad.mit.edu	37	20	5559094	5559094	+	Missense_Mutation	SNP	G	G	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:5559094G>T	ENST00000379019.4	-	8	849	c.637C>A	c.(637-639)Cgt>Agt	p.R213S	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	213					glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TCTGTCCAACGATCAGGCTGC	0.443																																						ENST00000379019.4																			0				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						c.(637-639)Cgt>Agt		glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)							123.0	108.0	114.0					20																	5559094		2203	4300	6503	SO:0001583	missense	56261				glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity	g.chr20:5559094G>T		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.637C>A	20.37:g.5559094G>T	ENSP00000368305:p.Arg213Ser					GPCPD1_ENST00000481038.1_5'UTR	p.R213S	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN			8	849	-			213					D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	37	c.637C>A	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827235	0.50739	.	.	ENSG00000125772	ENST00000379019	T	0.41400	1.0	5.35	5.35	0.76521	.	0.064339	0.64402	D	0.000003	T	0.43166	0.1235	L	0.29908	0.895	0.58432	D	0.999999	D	0.58268	0.982	P	0.49752	0.621	T	0.14896	-1.0456	10	0.32370	T	0.25	-5.4964	19.4355	0.94792	0.0:0.0:1.0:0.0	.	213	Q9NPB8	GPCP1_HUMAN	S	213	ENSP00000368305:R213S	ENSP00000368305:R213S	R	-	1	0	GPCPD1	5507094	1.000000	0.71417	0.830000	0.32933	0.914000	0.54420	6.636000	0.74299	2.668000	0.90789	0.655000	0.94253	CGT		0.443	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		4	75	1	0	0.000602214	1	0.000602214	4	75				
RYR3	6263	broad.mit.edu	37	15	34115225	34115225	+	Missense_Mutation	SNP	A	A	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr15:34115225A>G	ENST00000389232.4	+	81	11094	c.11024A>G	c.(11023-11025)aAg>aGg	p.K3675R	RYR3_ENST00000415757.3_Missense_Mutation_p.K3670R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3675					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAGGAGAAAAAGGATGCTGGA	0.418																																						ENST00000389232.4																			0				NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311						c.(11023-11025)aAg>aGg		ryanodine receptor 3							114.0	109.0	110.0					15																	34115225		1842	4107	5949	SO:0001583	missense	6263				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:34115225A>G		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.11024A>G	15.37:g.34115225A>G	ENSP00000373884:p.Lys3675Arg					RYR3_ENST00000415757.3_Missense_Mutation_p.K3670R	p.K3675R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	81	11094	+		all_lung(180;7.18e-09)	3675					O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	c.11024A>G	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.461181	0.43736	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.91351	-2.83	5.35	5.35	0.76521	.	0.056600	0.64402	D	0.000002	T	0.80314	0.4600	N	0.12182	0.205	0.30598	N	0.760798	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.73142	-0.4076	10	0.26408	T	0.33	.	9.91	0.41399	0.9246:0.0:0.0754:0.0	.	3670;3675	Q15413-2;Q15413	.;RYR3_HUMAN	R	3675;3674;3670	ENSP00000373884:K3675R	ENSP00000354735:K3670R	K	+	2	0	RYR3	31902517	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.735000	0.68587	2.243000	0.73865	0.533000	0.62120	AAG		0.418	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			3	52	0	0	0	1	0	3	52				
CPS1	1373	broad.mit.edu	37	2	211473267	211473267	+	Missense_Mutation	SNP	T	T	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:211473267T>C	ENST00000233072.5	+	19	2571	c.2375T>C	c.(2374-2376)aTg>aCg	p.M792T	CPS1_ENST00000451903.2_Missense_Mutation_p.M341T|CPS1_ENST00000430249.2_Missense_Mutation_p.M798T	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	792			M -> I (in CPS1D). {ECO:0000269|PubMed:21120950}.		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GGTAGCTCTATGAAAAGTGTA	0.418																																						ENST00000233072.5																			0				breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142						c.(2374-2376)aTg>aCg		carbamoyl-phosphate synthase 1, mitochondrial							125.0	122.0	123.0					2																	211473267		2203	4300	6503	SO:0001583	missense	1373				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity	g.chr2:211473267T>C	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2375T>C	2.37:g.211473267T>C	ENSP00000233072:p.Met792Thr					CPS1_ENST00000430249.2_Missense_Mutation_p.M798T|CPS1_ENST00000451903.2_Missense_Mutation_p.M341T	p.M792T	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN		Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	19	2571	+			792					B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	c.2375T>C	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173757	0.78452	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97976	-4.64;-4.64;-4.64	5.86	5.86	0.93980	ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.98406	0.9470	H	0.94847	3.59	0.80722	D	1	P;P	0.43938	0.822;0.822	P;P	0.45639	0.488;0.488	D	0.99616	1.0982	10	0.87932	D	0	-9.8479	16.5602	0.84551	0.0:0.0:0.0:1.0	.	802;792	Q59HF8;P31327	.;CPSM_HUMAN	T	798;800;792;341	ENSP00000402608:M798T;ENSP00000233072:M792T;ENSP00000406136:M341T	ENSP00000233072:M792T	M	+	2	0	CPS1	211181512	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.655000	0.83696	2.367000	0.80283	0.528000	0.53228	ATG		0.418	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			4	117	0	0	0	1	0	4	117				
CDH6	1004	broad.mit.edu	37	5	31299603	31299603	+	Nonsense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:31299603C>T	ENST00000265071.2	+	5	941	c.676C>T	c.(676-678)Cga>Tga	p.R226*	CDH6_ENST00000514738.1_Nonsense_Mutation_p.R171*	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CAACATGGATCGAGAAAACAG	0.438																																						ENST00000265071.2																			0				NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						c.(676-678)Cga>Tga		cadherin 6, type 2, K-cadherin (fetal kidney)							145.0	137.0	140.0					5																	31299603		2203	4300	6503	SO:0001587	stop_gained	1004				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding	g.chr5:31299603C>T	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.676C>T	5.37:g.31299603C>T	ENSP00000265071:p.Arg226*					CDH6_ENST00000514738.1_Nonsense_Mutation_p.R171*	p.R226*	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN			5	941	+			226			Cadherin 2.		A8K5H5|Q9BWS0	Nonsense_Mutation	SNP	ENST00000265071.2	37	c.676C>T	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	40	8.217388	0.98712	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	.	.	.	6.07	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1435	0.65334	0.3643:0.6357:0.0:0.0	.	.	.	.	X	171;226	.	ENSP00000265071:R226X	R	+	1	2	CDH6	31335360	0.941000	0.31946	1.000000	0.80357	0.993000	0.82548	0.091000	0.15046	2.885000	0.99019	0.655000	0.94253	CGA		0.438	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		4	82	0	0	0	1	0	4	82				
UVSSA	57654	broad.mit.edu	37	4	1343499	1343499	+	Missense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:1343499G>A	ENST00000389851.4	+	3	733	c.286G>A	c.(286-288)Gca>Aca	p.A96T	UVSSA_ENST00000511216.1_Missense_Mutation_p.A96T|UVSSA_ENST00000507531.1_Missense_Mutation_p.A96T	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	96	VHS-like.				protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										CACAGACCCCGCACAGCCTCT	0.627																																						ENST00000389851.4																			0											c.(286-288)Gca>Aca		UV-stimulated scaffold protein A							40.0	41.0	40.0					4																	1343499		2203	4300	6503	SO:0001583	missense	57654							g.chr4:1343499G>A	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.286G>A	4.37:g.1343499G>A	ENSP00000374501:p.Ala96Thr					UVSSA_ENST00000511216.1_Missense_Mutation_p.A96T|UVSSA_ENST00000507531.1_Missense_Mutation_p.A96T	p.A96T	NM_020894.2	NP_065945.2	Q2YD98	K1530_HUMAN			3	733	+			96					A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Missense_Mutation	SNP	ENST00000389851.4	37	c.286G>A	CCDS33938.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005437	0.35415	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531	T;T;T	0.22134	1.97;1.97;1.97	4.98	3.19	0.36642	.	0.276343	0.39687	N	0.001288	T	0.07234	0.0183	N	0.03608	-0.345	0.80722	D	1	P	0.41643	0.758	B	0.29077	0.098	T	0.29027	-1.0025	10	0.62326	D	0.03	.	9.2746	0.37692	0.076:0.0:0.7789:0.1451	.	96	Q2YD98	K1530_HUMAN	T	96	ENSP00000425130:A96T;ENSP00000374501:A96T;ENSP00000421741:A96T	ENSP00000374501:A96T	A	+	1	0	KIAA1530	1333499	0.990000	0.36364	0.015000	0.15790	0.076000	0.17211	3.472000	0.53114	0.464000	0.27142	0.655000	0.94253	GCA		0.627	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		3	47	0	0	0	1	0	3	47				
PCDHB5	26167	broad.mit.edu	37	5	140517245	140517245	+	Silent	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:140517245C>T	ENST00000231134.5	+	1	2446	c.2229C>T	c.(2227-2229)acC>acT	p.T743T		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	743					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCACCGGGACCCTATCCCAGA	0.642																																						ENST00000231134.5																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81						c.(2227-2229)acC>acT									96.0	115.0	109.0					5																	140517245		2203	4300	6503	SO:0001819	synonymous_variant	26167				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding	g.chr5:140517245C>T	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2229C>T	5.37:g.140517245C>T							p.T743T	NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	2446	+			743					Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	37	c.2229C>T	CCDS4247.1																																																																																				0.642	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		26	236	0	0	0	1	0	26	236				
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																						ENST00000374796.2																			15	Substitution - coding silent(15)	p.Q269Q(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(805-807)caG>caA		nuclear receptor coactivator 6							64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33345744C>T	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T						NCOA6_ENST00000359003.2_Silent_p.Q269Q	p.Q269Q			Q14686	NCOA6_HUMAN			8	3377	-			269			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	c.807G>A	CCDS13241.1																																																																																				0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		3	34	0	0	0	1	0	3	34				
BMS1P20	96610	broad.mit.edu	37	22	22661276	22661276	+	RNA	SNP	T	T	C	rs2329972	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr22:22661276T>C	ENST00000426066.1	+	0	360					NR_027293.1				BMS1 pseudogene 20																		GATGTACGTCTGCGTTGAGAT	0.488													.|||	7	0.00139776	0.0023	0.0	5008	,	,		18658	0.002		0.001	False		,,,				2504	0.001					ENST00000426066.1																			0																																																			96610							g.chr22:22661276T>C			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661276T>C								NR_027293.1						0	360	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.488	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			5	42	0	0	0	1	0	5	42				
HRG	3273	broad.mit.edu	37	3	186395480	186395480	+	Silent	SNP	T	T	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr3:186395480T>C	ENST00000232003.4	+	7	1466	c.1386T>C	c.(1384-1386)ccT>ccC	p.P462P		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	462	His/Pro-rich (HRR).				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		ACCGACTCCCTCCTCTAAGAA	0.552																																						ENST00000232003.4																			0				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						c.(1384-1386)ccT>ccC		histidine-rich glycoprotein							100.0	98.0	99.0					3																	186395480		2203	4300	6503	SO:0001819	synonymous_variant	3273				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding	g.chr3:186395480T>C		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1386T>C	3.37:g.186395480T>C							p.P462P	NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)	7	1466	+	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		462			His/Pro-rich (HRR).		B9EK35|D3DNU7	Silent	SNP	ENST00000232003.4	37	c.1386T>C	CCDS3280.1																																																																																				0.552	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		37	30	0	0	0	1	0	37	30				
DNM1P47	100216544	broad.mit.edu	37	15	102304884	102304884	+	RNA	SNP	G	G	C	rs192934815		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr15:102304884G>C	ENST00000561463.1	+	0	12930									DNM1 pseudogene 47																		GCGTGGGAACGAGAAGACACT	0.562																																						ENST00000561463.1																			0																																																			100216544							g.chr15:102304884G>C	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304884G>C														0	12930	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.562	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	17	0	0	0	1	0	3	17				
CRB2	286204	broad.mit.edu	37	9	126133381	126133381	+	Missense_Mutation	SNP	G	G	A	rs372093386		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr9:126133381G>A	ENST00000373631.3	+	8	1961	c.1960G>A	c.(1960-1962)Gcc>Acc	p.A654T	CRB2_ENST00000359999.3_Missense_Mutation_p.A654T|CRB2_ENST00000373629.2_Missense_Mutation_p.A322T	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	654	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CTTGGGAGGCGCCCCAAGCTC	0.617																																						ENST00000373631.3																			0				NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						c.(1960-1962)Gcc>Acc		crumbs homolog 2 (Drosophila)		G	THR/ALA	1,4405		0,1,2202	81.0	91.0	87.0		1960	-5.9	0.0	9		87	0,8600		0,0,4300	no	missense	CRB2	NM_173689.5	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	654/1286	126133381	1,13005	2203	4300	6503	SO:0001583	missense	286204					extracellular region|integral to membrane|plasma membrane	calcium ion binding	g.chr9:126133381G>A	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.1960G>A	9.37:g.126133381G>A	ENSP00000362734:p.Ala654Thr					CRB2_ENST00000373629.2_Missense_Mutation_p.A322T|CRB2_ENST00000359999.3_Missense_Mutation_p.A654T	p.A654T	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN			8	1961	+			654			Laminin G-like 2.		A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	c.1960G>A	CCDS6852.2	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.889265	0.00527	2.27E-4	0.0	ENSG00000148204	ENST00000359999;ENST00000373631;ENST00000373629	T;T;T	0.79033	-1.23;-1.23;-1.23	5.16	-5.86	0.02304	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	1.130590	0.06759	N	0.781497	T	0.45054	0.1323	N	0.02865	-0.47	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.06405	0.001;0.002	T	0.51671	-0.8676	10	0.02654	T	1	.	8.2962	0.31986	0.3099:0.0:0.5411:0.149	.	654;654	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	T	654;654;322	ENSP00000353092:A654T;ENSP00000362734:A654T;ENSP00000362732:A322T	ENSP00000353092:A654T	A	+	1	0	CRB2	125173202	0.000000	0.05858	0.038000	0.18304	0.046000	0.14306	-0.010000	0.12743	-0.361000	0.08125	-1.079000	0.02226	GCC		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		4	138	0	0	0	1	0	4	138				
ANGPTL2	23452	broad.mit.edu	37	9	129870241	129870241	+	Missense_Mutation	SNP	G	G	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr9:129870241G>C	ENST00000373425.3	-	2	1387	c.770C>G	c.(769-771)aCt>aGt	p.T257S	RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000491991.1_5'UTR|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000373436.1_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	257					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						AGTGGGCATAGTGGGCAGAGG	0.577																																						ENST00000373425.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						c.(769-771)aCt>aGt		angiopoietin-like 2							109.0	106.0	107.0					9																	129870241		2203	4300	6503	SO:0001583	missense	23452				multicellular organismal development|signal transduction	extracellular space	receptor binding	g.chr9:129870241G>C	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.770C>G	9.37:g.129870241G>C	ENSP00000362524:p.Thr257Ser					RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000491991.1_5'UTR|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000259351.5_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000373434.1_Intron	p.T257S	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN			2	1387	-			257					Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	37	c.770C>G	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.939389	0.34189	.	.	ENSG00000136859	ENST00000373425	T	0.46451	0.87	5.32	5.32	0.75619	.	0.467757	0.23120	N	0.051710	T	0.36717	0.0977	L	0.43152	1.355	0.80722	D	1	B	0.28900	0.227	B	0.30316	0.114	T	0.19095	-1.0316	10	0.07030	T	0.85	.	19.3588	0.94425	0.0:0.0:1.0:0.0	.	257	Q9UKU9	ANGL2_HUMAN	S	257	ENSP00000362524:T257S	ENSP00000362524:T257S	T	-	2	0	ANGPTL2	128910062	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.660000	0.98599	2.640000	0.89533	0.655000	0.94253	ACT		0.577	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		26	52	0	0	0	1	0	26	52				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977327	29977327	+	RNA	SNP	T	T	C	rs200662795		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:29977327T>C	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		GACAGCTGCCTTGTGTGGGAC	0.438																																						ENST00000376797.3																			0																																																			80862							g.chr6:29977327T>C	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977327T>C						HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.438	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		4	94	0	0	0	1	0	4	94				
DHX29	54505	broad.mit.edu	37	5	54579230	54579230	+	Missense_Mutation	SNP	C	C	T	rs187247676		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:54579230C>T	ENST00000251636.5	-	11	1914	c.1766G>A	c.(1765-1767)cGg>cAg	p.R589Q	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	589	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AACCACTACCCGATGCCTTTT	0.398													C|||	1	0.000199681	0.0	0.0	5008	,	,		20488	0.0		0.001	False		,,,				2504	0.0					ENST00000251636.5																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46						c.(1765-1767)cGg>cAg		DEAH (Asp-Glu-Ala-His) box polypeptide 29		C	GLN/ARG	0,4406		0,0,2203	121.0	128.0	125.0		1766	4.9	1.0	5		125	2,8596	2.2+/-6.3	0,2,4297	yes	missense	DHX29	NM_019030.2	43	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	589/1370	54579230	2,13002	2203	4299	6502	SO:0001583	missense	54505						ATP binding|ATP-dependent helicase activity|translation initiation factor activity	g.chr5:54579230C>T	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.1766G>A	5.37:g.54579230C>T	ENSP00000251636:p.Arg589Gln					RP11-506H20.1_ENST00000506435.1_RNA	p.R589Q	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN			11	1914	-		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)	589			Helicase ATP-binding.		O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Missense_Mutation	SNP	ENST00000251636.5	37	c.1766G>A	CCDS34158.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.02	2.111602	0.37242	0.0	2.33E-4	ENSG00000067248	ENST00000251636	T	0.03982	3.74	5.74	4.87	0.63330	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.114438	0.64402	D	0.000018	T	0.01254	0.0041	N	0.00427	-1.505	0.44366	D	0.99726	P	0.42375	0.778	B	0.31946	0.138	T	0.55541	-0.8125	10	0.05620	T	0.96	.	16.713	0.85389	0.0:0.8704:0.1296:0.0	.	589	Q7Z478	DHX29_HUMAN	Q	589	ENSP00000251636:R589Q	ENSP00000251636:R589Q	R	-	2	0	DHX29	54614987	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	4.707000	0.61852	1.409000	0.46915	-0.282000	0.10007	CGG		0.398	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030		5	202	0	0	0	1	0	5	202				
PSMA7	5688	broad.mit.edu	37	20	60715937	60715937	+	Nonsense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:60715937G>A	ENST00000370873.4	-	2	286	c.160C>T	c.(160-162)Cag>Tag	p.Q54*	PSMA7_ENST00000370861.1_5'UTR|PSMA7_ENST00000370858.3_Nonsense_Mutation_p.Q54*|SS18L1_ENST00000331758.3_5'Flank|PSMA7_ENST00000484488.1_5'UTR|SS18L1_ENST00000421564.1_5'Flank	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	54					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CTTTCATCCTGCAGTTTGGCC	0.468																																						ENST00000370873.4																			0				large_intestine(1)|lung(2)	3						c.(160-162)Cag>Tag		proteasome (prosome, macropain) subunit, alpha type, 7							280.0	192.0	222.0					20																	60715937		2203	4300	6503	SO:0001587	stop_gained	5688				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity	g.chr20:60715937G>A	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"""Proteasome (prosome, macropain) subunits"""	9536	protein-coding gene	gene with protein product	"""proteasome subunit XAPC7"", ""proteasome subunit RC6-1"""	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.160C>T	20.37:g.60715937G>A	ENSP00000359910:p.Gln54*					PSMA7_ENST00000370861.1_5'UTR|PSMA7_ENST00000370858.3_Nonsense_Mutation_p.Q54*|PSMA7_ENST00000484488.1_5'UTR	p.Q54*	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	BRCA - Breast invasive adenocarcinoma(19;1.28e-07)		2	286	-	Breast(26;3.97e-09)		54					B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Nonsense_Mutation	SNP	ENST00000370873.4	37	c.160C>T	CCDS13489.1	.	.	.	.	.	.	.	.	.	.	G	38	6.669228	0.97747	.	.	ENSG00000101182	ENST00000370873;ENST00000370858	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.3625	0.94446	0.0:0.0:1.0:0.0	.	.	.	.	X	54	.	ENSP00000359895:Q54X	Q	-	1	0	PSMA7	60149332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.381000	0.97205	2.568000	0.86640	0.655000	0.94253	CAG		0.468	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		60	94	0	0	0	1	0	60	94				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977342	29977342	+	RNA	SNP	A	A	T	rs113017032	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:29977342A>T	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		TGGGACTGAGAGGCAAGATTT	0.438													A|||	16	0.00319489	0.003	0.0029	5008	,	,		21762	0.0		0.003	False		,,,				2504	0.0072					ENST00000376797.3																			0																																																			80862							g.chr6:29977342A>T	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977342A>T						HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.438	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		5	86	0	0	0	1	0	5	86				
RET	5979	broad.mit.edu	37	10	43617416	43617416	+	Missense_Mutation	SNP	T	T	C	rs74799832		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr10:43617416T>C	ENST00000355710.3	+	16	2985	c.2753T>C	c.(2752-2754)aTg>aCg	p.M918T	RET_ENST00000340058.5_Missense_Mutation_p.M918T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	918	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		M -> T (in MEN2B and MTC; sporadic form; somatic mutation; also found in a patient with renal agenesis; dbSNP:rs74799832). {ECO:0000269|PubMed:18252215, ECO:0000269|PubMed:7906417, ECO:0000269|PubMed:7906866, ECO:0000269|PubMed:7911697, ECO:0000269|PubMed:8595427, ECO:0000269|PubMed:8807338}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.M918T(247)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GTTAAATGGATGGCAATTGAA	0.443		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	ENST00000355710.3		1	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	"""T, Mis, N, F"""	ret proto-oncogene	yes	Hirschsprung disease	"""E, O"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	CCDC6/RET(4)|KIF5B/RET(79)	247	Substitution - Missense(247)	p.M918T(247)	thyroid(231)|adrenal_gland(16)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607	GRCh37	CM941246	RET	M	rs74799832	c.(2752-2754)aTg>aCg		ret proto-oncogene	Sunitinib(DB01268)						262.0	244.0	250.0					10																	43617416		2203	4300	6503	SO:0001583	missense	5979	Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development	integral to membrane	ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity	g.chr10:43617416T>C	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2753T>C	10.37:g.43617416T>C	ENSP00000347942:p.Met918Thr					RET_ENST00000340058.5_Missense_Mutation_p.M918T	p.M918T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN			16	2985	+		Ovarian(717;0.0423)	918		M -> T (in RADYS, MEN2B and MTC; sporadic form; somatic mutation).	Protein kinase.		A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	c.2753T>C	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.427864	0.83667	.	.	ENSG00000165731	ENST00000355710;ENST00000340058	D;D	0.90504	-2.68;-2.68	5.43	5.43	0.79202	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93719	0.7993	L	0.52126	1.63	0.80722	A	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94557	0.7759	9	0.87932	D	0	.	15.7766	0.78224	0.0:0.0:0.0:1.0	.	664;918;918	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	T	918	ENSP00000347942:M918T;ENSP00000344798:M918T	ENSP00000344798:M918T	M	+	2	0	RET	42937422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.986000	0.88173	2.198000	0.70561	0.533000	0.62120	ATG		0.443	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		53	131	0	0	0	1	0	53	131				
GC	2638	broad.mit.edu	37	4	72629626	72629626	+	Silent	SNP	G	G	A	rs149884974	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:72629626G>A	ENST00000273951.8	-	5	844	c.501C>T	c.(499-501)taC>taT	p.Y167Y	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Silent_p.Y186Y|GC_ENST00000513476.1_Silent_p.Y167Y	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	167	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)	p.Y167Y(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	GAGCTTGTCCGTAATTAGTGG	0.363													g|||	2	0.000399361	0.0015	0.0	5008	,	,		17704	0.0		0.0	False		,,,				2504	0.0					ENST00000273951.8																			1	Substitution - coding silent(1)	p.Y167Y(1)	prostate(1)	endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45						c.(499-501)taC>taT		group-specific component (vitamin D binding protein)	Cholecalciferol(DB00169)	A	,,	12,4394	19.1+/-41.9	0,12,2191	84.0	87.0	86.0		501,501,558	-1.2	1.0	4	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GC	NM_000583.3,NM_001204306.1,NM_001204307.1	,,	0,12,6491	AA,AG,GG		0.0,0.2724,0.0923	,,	167/475,167/475,186/494	72629626	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	2638				hormone biosynthetic process|vitamin D metabolic process	cytosol|lysosomal lumen	actin binding|vitamin D binding|vitamin transporter activity	g.chr4:72629626G>A	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.501C>T	4.37:g.72629626G>A						GC_ENST00000503472.1_5'UTR|GC_ENST00000513476.1_Silent_p.Y167Y|GC_ENST00000504199.1_Silent_p.Y186Y	p.Y167Y	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	Lung(101;0.148)		5	844	-		all_hematologic(202;0.107)	167			Albumin 1.		B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	37	c.501C>T	CCDS3550.1																																																																																				0.363	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			9	83	0	0	0	1	0	9	83				
FOS	2353	broad.mit.edu	37	14	75746642	75746642	+	Silent	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr14:75746642G>A	ENST00000303562.4	+	2	413	c.204G>A	c.(202-204)tcG>tcA	p.S68S	FOS_ENST00000554617.1_Silent_p.S68S|FOS_ENST00000555686.1_5'UTR|FOS_ENST00000535987.1_Silent_p.S68S|FOS_ENST00000555242.1_Silent_p.S68S|FOS_ENST00000555347.1_5'Flank	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN	FBJ murine osteosarcoma viral oncogene homolog	68					aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hormone stimulus (GO:0032870)|cellular response to reactive oxygen species (GO:0034614)|conditioned taste aversion (GO:0001661)|DNA methylation (GO:0006306)|Fc-epsilon receptor signaling pathway (GO:0038095)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gravity (GO:0009629)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|skeletal muscle cell differentiation (GO:0035914)|sleep (GO:0030431)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	double-stranded DNA binding (GO:0003690)|R-SMAD binding (GO:0070412)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)	Nadroparin(DB08813)|Pseudoephedrine(DB00852)	CTGCCATCTCGACCAGTCCGG	0.642																																						ENST00000303562.4																			0				central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						c.(202-204)tcG>tcA		FBJ murine osteosarcoma viral oncogene homolog							87.0	85.0	86.0					14																	75746642		2203	4300	6503	SO:0001819	synonymous_variant	2353				cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway		protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding	g.chr14:75746642G>A	K00650	CCDS9841.1	14q24.3	2013-01-10	2009-07-23			ENSG00000170345		"""basic leucine zipper proteins"""	3796	protein-coding gene	gene with protein product		164810	"""v-fos FBJ murine osteosarcoma viral oncogene homolog"""			16123044, 16055710, 15926923	Standard	NM_005252		Approved	c-fos, AP-1	uc001xrn.3	P01100		ENST00000303562.4:c.204G>A	14.37:g.75746642G>A						FOS_ENST00000555686.1_5'UTR|FOS_ENST00000535987.1_Silent_p.S68S|FOS_ENST00000555242.1_Silent_p.S68S|FOS_ENST00000554617.1_Silent_p.S68S	p.S68S	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.0117)	2	413	+		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)	68					A8K4E2|B4DQ65|P18849	Silent	SNP	ENST00000303562.4	37	c.204G>A	CCDS9841.1	.	.	.	.	.	.	.	.	.	.	G	3.550	-0.091893	0.07053	.	.	ENSG00000170345	ENST00000554212	.	.	.	5.95	-11.9	0.00025	.	.	.	.	.	T	0.47414	0.1444	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63743	-0.6568	4	.	.	.	-1.3749	10.8872	0.46974	0.2105:0.5964:0.0795:0.1136	.	.	.	.	N	59	.	.	D	+	1	0	FOS	74816395	0.002000	0.14202	0.231000	0.23993	0.648000	0.38561	-1.555000	0.02170	-2.779000	0.00361	-2.169000	0.00324	GAC		0.642	FOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415044.1	NM_005252		4	80	0	0	0	1	0	4	80				
OTOP1	133060	broad.mit.edu	37	4	4228274	4228282	+	In_Frame_Del	DEL	CCACAGCAG	CCACAGCAG	-	rs75328065|rs199840382|rs111245977|rs377667898|rs200554408|rs201436152	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:4228274_4228282delCCACAGCAG	ENST00000296358.4	-	1	334_342	c.310_318delCTGCTGTGG	c.(310-318)ctgctgtggdel	p.LLW104del		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	104					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.L104_W106delLLW(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACCACAGCATCCACAGCAGCTGCAGCAGC	0.727																																						ENST00000296358.4																			1	Deletion - In frame(1)	p.L104_W106delLLW(1)	upper_aerodigestive_tract(1)	NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						c.(310-318)del		otopetrin 1																																				SO:0001651	inframe_deletion	133060				biomineral tissue development	extracellular space|integral to membrane		g.chr4:4228274_4228282delCCACAGCAG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.310_318delCTGCTGTGG	4.37:g.4228274_4228282delCCACAGCAG	ENSP00000296358:p.Leu104_Trp106del						p.LLW104del	NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	1	334_342	-			104					A1L476	In_Frame_Del	DEL	ENST00000296358.4	37	c.310_318delCTGCTGTGG	CCDS3372.1																																																																																				0.727	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		9	27						9	27	---	---	---	---
SUDS3P1	285647	broad.mit.edu	37	5	177398373	177398396	+	RNA	DEL	AGGACGAAGAGCTGGAGAGCGCCA	AGGACGAAGAGCTGGAGAGCGCCA	-	rs548039666|rs70994948|rs71585660|rs568597025|rs535774316	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA	ENST00000511650.1	+	0	145																											GTCCCCGGGGAGGACGAAGAGCTGGAGAGCGCCAAGGACGACGA	0.683														1220	0.24361	0.2678	0.3372	5008	,	,		15351	0.1548		0.2674	False		,,,				2504	0.2117					ENST00000511650.1																			0																																																			285647							g.chr5:177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA																													5.37:g.177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA														0	145	+									RNA	DEL	ENST00000511650.1	37																																																																																						0.683	RP11-1252I4.2-001	KNOWN	basic	antisense	antisense	OTTHUMT00000373553.1			3	3						3	3	---	---	---	---
