#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
NID2	22795	broad.mit.edu	37	14	52508861	52508861	+	Nonsense_Mutation	SNP	A	A	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr14:52508861A>T	ENST00000216286.5	-	7	1786	c.1787T>A	c.(1786-1788)tTa>tAa	p.L596*	NID2_ENST00000541773.1_Nonsense_Mutation_p.L543*	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	596	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					AGGTTTTTCTAAAGCAAAGAG	0.602																																						ENST00000216286.5																			0				NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87						c.(1786-1788)tTa>tAa		nidogen 2 (osteonidogen)							88.0	97.0	94.0					14																	52508861		2203	4300	6503	SO:0001587	stop_gained	22795					basement membrane	calcium ion binding|collagen binding	g.chr14:52508861A>T	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1787T>A	14.37:g.52508861A>T	ENSP00000216286:p.Leu596*					NID2_ENST00000541773.1_Nonsense_Mutation_p.L543*	p.L596*	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN			7	1786	-	Breast(41;0.0639)|all_epithelial(31;0.123)		596			Nidogen G2 beta-barrel.		A8K6I7|B4DU19|O43710	Nonsense_Mutation	SNP	ENST00000216286.5	37	c.1787T>A	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	A	41	8.966905	0.99019	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0558	0.80805	1.0:0.0:0.0:0.0	.	.	.	.	X	596;190;543;598	.	ENSP00000216286:L596X	L	-	2	0	NID2	51578611	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.806000	0.91930	2.281000	0.76405	0.533000	0.62120	TTA		0.602	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			37	69	0	0	0	1	0	37	69				
GJB2	2706	broad.mit.edu	37	13	20763342	20763342	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr13:20763342G>A	ENST00000382844.1	-	1	577	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	GJB2_ENST00000382848.4_Missense_Mutation_p.R127C			P29033	CXB2_HUMAN	gap junction protein, beta 2, 26kDa	127			R -> H (very common polymorphism in India; dbSNP:rs111033196). {ECO:0000269|PubMed:12746422, ECO:0000269|PubMed:14722929, ECO:0000269|PubMed:15666300}.		cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_cancers(29;3.95e-22)|all_epithelial(30;2.36e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000435)|Epithelial(112;0.000722)|OV - Ovarian serous cystadenocarcinoma(117;0.0096)|Lung(94;0.0236)|LUSC - Lung squamous cell carcinoma(192;0.0738)		CCTTCGATGCGGACCTTCTGG	0.512									Keratitis, Ichthyosis and Deafness syndrome		OREG0022282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000382844.1																			0				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7	GRCh37	CM014710	GJB2	M		c.(379-381)Cgc>Tgc		gap junction protein, beta 2, 26kDa							114.0	107.0	109.0					13																	20763342		2203	4300	6503	SO:0001583	missense	0	Keratitis, Ichthyosis and Deafness syndrome	Familial Cancer Database	KID syndrome	cell-cell signaling|cellular membrane organization|gap junction assembly|sensory perception of sound|transport	connexon complex|ER-Golgi intermediate compartment|integral to membrane		g.chr13:20763342G>A	M86849	CCDS9290.1	13q11-q12	2010-01-06	2007-01-16		ENSG00000165474	ENSG00000165474		"""Ion channels / Gap junction proteins (connexins)"""	4284	protein-coding gene	gene with protein product	"""connexin 26"""	121011	"""gap junction protein, beta 2, 26kD (connexin 26)"", ""gap junction protein, beta 2, 26kDa (connexin 26)"""	DFNB1, DFNA3		9139825	Standard	NM_004004		Approved	CX26, NSRD1	uc001umy.3	P29033	OTTHUMG00000016513	ENST00000382844.1:c.379C>T	13.37:g.20763342G>A	ENSP00000372295:p.Arg127Cys		OREG0022282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	743	GJB2_ENST00000382848.4_Missense_Mutation_p.R127C	p.R127C			P29033	CXB2_HUMAN		all cancers(112;0.000435)|Epithelial(112;0.000722)|OV - Ovarian serous cystadenocarcinoma(117;0.0096)|Lung(94;0.0236)|LUSC - Lung squamous cell carcinoma(192;0.0738)	1	577	-		all_cancers(29;3.95e-22)|all_epithelial(30;2.36e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)	127		R -> H (very common polymorphism in India).			Q508A5|Q508A6|Q5YLL0|Q5YLL1|Q5YLL4|Q6IPV5|Q86U88|Q96AK0|Q9H536|Q9NNY4	Missense_Mutation	SNP	ENST00000382844.1	37	c.379C>T	CCDS9290.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.694148	0.68386	.	.	ENSG00000165474	ENST00000382848;ENST00000382844	D;D	0.97791	-4.54;-4.54	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000002	D	0.96188	0.8757	L	0.55481	1.735	0.80722	D	1	D	0.64830	0.994	B	0.43536	0.423	D	0.95978	0.8975	10	0.56958	D	0.05	.	14.5272	0.67897	0.0:0.0:0.8535:0.1465	.	127	P29033	CXB2_HUMAN	C	127	ENSP00000372299:R127C;ENSP00000372295:R127C	ENSP00000372295:R127C	R	-	1	0	GJB2	19661342	0.998000	0.40836	0.999000	0.59377	0.862000	0.49288	4.443000	0.59994	2.723000	0.93209	0.655000	0.94253	CGC		0.512	GJB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044064.1			27	51	0	0	0	1	0	27	51				
AIFM3	150209	broad.mit.edu	37	22	21327704	21327704	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr22:21327704G>A	ENST00000399167.2	+	3	380	c.140G>A	c.(139-141)cGc>cAc	p.R47H	AIFM3_ENST00000399163.2_Missense_Mutation_p.R47H|AIFM3_ENST00000333607.6_Missense_Mutation_p.R47H|AIFM3_ENST00000405089.1_Missense_Mutation_p.R53H|AIFM3_ENST00000440238.2_Missense_Mutation_p.R47H|AIFM3_ENST00000335375.5_Missense_Mutation_p.A72T	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	47					cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GGCACGGCCCGCCACTTCCAC	0.662																																						ENST00000399167.2																			0				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21						c.(139-141)cGc>cAc		apoptosis-inducing factor, mitochondrion-associated, 3							23.0	24.0	24.0					22																	21327704		2202	4297	6499	SO:0001583	missense	150209							g.chr22:21327704G>A	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.140G>A	22.37:g.21327704G>A	ENSP00000382120:p.Arg47His					AIFM3_ENST00000399163.2_Missense_Mutation_p.R47H|AIFM3_ENST00000333607.6_Missense_Mutation_p.R47H|AIFM3_ENST00000405089.1_Missense_Mutation_p.R53H|AIFM3_ENST00000335375.5_Missense_Mutation_p.A72T|AIFM3_ENST00000440238.2_Missense_Mutation_p.R47H	p.R47H	NM_144704.2	NP_653305.1			LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		3	380	+	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)						B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	c.140G>A	CCDS13786.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.47|18.47	3.630318|3.630318	0.67015|0.67015	.|.	.|.	ENSG00000183773|ENSG00000183773	ENST00000335375|ENST00000399167;ENST00000399163;ENST00000441376;ENST00000434714;ENST00000405089;ENST00000440238;ENST00000333607	T|T;T;T;T;T	0.56103|0.51071	0.48|0.73;0.73;0.72;0.73;0.73	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	.|0.065074	.|0.64402	.|D	.|0.000007	T|T	0.41396|0.41396	0.1157|0.1157	N|N	0.19112|0.19112	0.55|0.55	0.47374|0.47374	D|D	0.999407|0.999407	B|D;D;D	0.31519|0.69078	0.327|0.997;0.994;0.997	B|P;P;P	0.21151|0.47744	0.033|0.556;0.556;0.469	T|T	0.38222|0.38222	-0.9671|-0.9671	9|10	0.87932|0.48119	D|T	0|0.1	-8.8417|-8.8417	16.1564|16.1564	0.81670|0.81670	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	72|53;47;47	B7Z9S7|Q96NN9-2;Q96NN9-3;Q96NN9	.|.;.;AIFM3_HUMAN	T|H	72|47;47;47;47;53;47;47	ENSP00000335369:A72T|ENSP00000382120:R47H;ENSP00000382116:R47H;ENSP00000385800:R53H;ENSP00000390798:R47H;ENSP00000327671:R47H	ENSP00000335369:A72T|ENSP00000327671:R47H	A|R	+|+	1|2	0|0	AIFM3|AIFM3	19657704|19657704	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.518000|0.518000	0.34316|0.34316	5.187000|5.187000	0.65087|0.65087	2.394000|2.394000	0.81467|0.81467	0.650000|0.650000	0.86243|0.86243	GCC|CGC		0.662	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704		7	8	0	0	0	1	0	7	8				
TTC3	7267	broad.mit.edu	37	21	38536463	38536463	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr21:38536463G>A	ENST00000399017.2	+	32	6028	c.3281G>A	c.(3280-3282)cGc>cAc	p.R1094H	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.R1094H|TTC3_ENST00000354749.2_Missense_Mutation_p.R1094H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1094					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TATGTTGTCCGCAATAAGAAG	0.393																																					Ovarian(38;194 1649 35661)	ENST00000399017.2																			0				breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75						c.(3280-3282)cGc>cAc		tetratricopeptide repeat domain 3							84.0	77.0	79.0					21																	38536463		2203	4300	6503	SO:0001583	missense	7267				protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr21:38536463G>A	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3281G>A	21.37:g.38536463G>A	ENSP00000381981:p.Arg1094His					TTC3_ENST00000354749.2_Missense_Mutation_p.R1094H|TTC3_ENST00000355666.1_Missense_Mutation_p.R1094H|TTC3_ENST00000479930.1_3'UTR	p.R1094H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN			32	6028	+		Myeloproliferative disorder(46;0.0412)	1094					A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	c.3281G>A	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.52|15.52	2.858057|2.858057	0.51376|0.51376	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T;T;T	.|0.12255	.|2.7;2.7;3.05;3.05;3.05	4.92|4.92	2.66|2.66	0.31614|0.31614	.|.	.|0.390747	.|0.20615	.|N	.|0.088890	T|T	0.26048|0.26048	0.0635|0.0635	L|L	0.57536|0.57536	1.79|1.79	0.22666|0.22666	N|N	0.998871|0.998871	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.74023	.|0.982;0.869	T|T	0.02546|0.02546	-1.1143|-1.1143	5|10	.|0.52906	.|T	.|0.07	-5.9888|-5.9888	4.9199|4.9199	0.13865|0.13865	0.3454:0.0:0.6546:0.0|0.3454:0.0:0.6546:0.0	.|.	.|152;1094	.|Q5GIT6;P53804	.|.;TTC3_HUMAN	T|H	250|1094;1076;1094;1094;1094	.|ENSP00000403943:R1094H;ENSP00000391891:R1076H;ENSP00000347889:R1094H;ENSP00000381981:R1094H;ENSP00000346791:R1094H	.|ENSP00000346791:R1094H	A|R	+|+	1|2	0|0	TTC3|TTC3	37458333|37458333	0.000000|0.000000	0.05858|0.05858	0.882000|0.882000	0.34594|0.34594	0.975000|0.975000	0.68041|0.68041	0.380000|0.380000	0.20602|0.20602	1.204000|1.204000	0.43247|0.43247	0.591000|0.591000	0.81541|0.81541	GCA|CGC		0.393	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			19	40	0	0	0	1	0	19	40				
POTEA	340441	broad.mit.edu	37	8	43157186	43157186	+	RNA	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr8:43157186G>A	ENST00000522175.2	+	0	697				RNU6-104P_ENST00000459597.1_RNA			Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCAAAATATTGATGTATTTTC	0.318																																						ENST00000522175.2																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46								POTE ankyrin domain family, member A							97.0	105.0	102.0					8																	43157186		2108	4255	6363			340441							g.chr8:43157186G>A	AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33893	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 3"""	608915	"""ANKRD26-like family A, member 1"""	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		8.37:g.43157186G>A										Q6S8J7	POTEA_HUMAN			0	697	+								A6ND17|A6ND71|Q6S8J6	RNA	SNP	ENST00000522175.2	37																																																																																						0.318	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1	NM_001002920		52	180	0	0	0	1	0	52	180				
OR4A47	403253	broad.mit.edu	37	11	48510647	48510647	+	Silent	SNP	C	C	T	rs201991606		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr11:48510647C>T	ENST00000446524.1	+	1	379	c.303C>T	c.(301-303)atC>atT	p.I101I		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						AGCTCTTTATCGAGCACATTT	0.428													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20992	0.0		0.0	False		,,,				2504	0.0					ENST00000446524.1																			0				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						c.(301-303)atC>atT		olfactory receptor, family 4, subfamily A, member 47							102.0	97.0	99.0					11																	48510647		2201	4298	6499	SO:0001819	synonymous_variant	403253				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:48510647C>T	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.303C>T	11.37:g.48510647C>T							p.I101I	NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN			1	379	+			101						Silent	SNP	ENST00000446524.1	37	c.303C>T	CCDS31490.1																																																																																				0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		46	65	0	0	0	1	0	46	65				
PNPLA7	375775	broad.mit.edu	37	9	140392628	140392628	+	Silent	SNP	G	G	A	rs367620575		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr9:140392628G>A	ENST00000277531.4	-	16	1938	c.1752C>T	c.(1750-1752)ttC>ttT	p.F584F	PNPLA7_ENST00000406427.1_Silent_p.F609F|PNPLA7_ENST00000371457.1_Silent_p.F190F	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	584					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TTTGCCGCACGAAGGACGACA	0.632																																						ENST00000406427.1																			0				breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						c.(1825-1827)ttC>ttT		patatin-like phospholipase domain containing 7		G	,	1,4401	2.1+/-5.4	0,1,2200	157.0	118.0	131.0		1827,1752	-1.8	1.0	9		131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,	609/1343,584/1318	140392628	1,13001	2201	4300	6501	SO:0001819	synonymous_variant	375775				lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity	g.chr9:140392628G>A	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.1752C>T	9.37:g.140392628G>A						PNPLA7_ENST00000277531.4_Silent_p.F584F|PNPLA7_ENST00000371457.1_Silent_p.F190F	p.F609F	NM_001098537.1	NP_001092007.1	Q6ZV29	PLPL7_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)	17	2163	-	all_cancers(76;0.126)		584					B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	c.1827C>T	CCDS7045.1																																																																																				0.632	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		10	32	0	0	0	1	0	10	32				
PCDHA12	56137	broad.mit.edu	37	5	140257309	140257309	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr5:140257309C>T	ENST00000398631.2	+	1	2252	c.2252C>T	c.(2251-2253)tCg>tTg	p.S751L	PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	751	5 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTCTTACTCGCAGCAGAGG	0.647																																					Pancreas(113;759 1672 13322 24104 50104)	ENST00000398631.2																			0				NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78						c.(2251-2253)tCg>tTg									32.0	33.0	32.0					5																	140257309		2203	4300	6503	SO:0001583	missense	0							g.chr5:140257309C>T	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.2252C>T	5.37:g.140257309C>T	ENSP00000381628:p.Ser751Leu					PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron	p.S751L	NM_018903.2|NM_031864.1	NP_061726.1|NP_114070.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	2252	+								O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	c.2252C>T	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443798	0.43429	.	.	ENSG00000251664	ENST00000398631	T	0.20463	2.07	4.88	4.0	0.46444	.	.	.	.	.	T	0.55081	0.1898	H	0.96015	3.755	0.23528	N	0.997489	D;D	0.71674	0.998;0.99	D;B	0.70716	0.97;0.426	T	0.54111	-0.8342	9	0.33141	T	0.24	.	9.8526	0.41066	0.0:0.7791:0.1418:0.0791	.	751;751	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	L	751	ENSP00000381628:S751L	ENSP00000381628:S751L	S	+	2	0	PCDHA12	140237493	0.001000	0.12720	0.005000	0.12908	0.076000	0.17211	0.181000	0.16880	1.017000	0.39495	0.655000	0.94253	TCG		0.647	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		17	24	0	0	0	1	0	17	24				
SAMD9	54809	broad.mit.edu	37	7	92735120	92735120	+	Silent	SNP	T	T	C			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr7:92735120T>C	ENST00000379958.2	-	3	560	c.291A>G	c.(289-291)aaA>aaG	p.K97K		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	97						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGTTTGGTCTTTAGGAGCAT	0.378																																						ENST00000379958.2																			0				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						c.(289-291)aaA>aaG		sterile alpha motif domain containing 9							177.0	174.0	175.0					7																	92735120		2203	4300	6503	SO:0001819	synonymous_variant	54809					cytoplasm		g.chr7:92735120T>C	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.291A>G	7.37:g.92735120T>C							p.K97K	NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	STAD - Stomach adenocarcinoma(171;0.000302)		3	560	-	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		97					A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	c.291A>G	CCDS34680.1																																																																																				0.378	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		68	166	0	0	0	1	0	68	166				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	5	52	0	0	0	1	0	5	52				
ANKRD52	283373	broad.mit.edu	37	12	56646642	56646642	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr12:56646642T>C	ENST00000267116.7	-	12	1344	c.1223A>G	c.(1222-1224)cAt>cGt	p.H408R		NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	408										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						TGAAAGCACATGCTCATTGCT	0.522																																						ENST00000267116.7																			0				endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						c.(1222-1224)cAt>cGt		ankyrin repeat domain 52							57.0	58.0	58.0					12																	56646642		2100	4241	6341	SO:0001583	missense	283373						protein binding	g.chr12:56646642T>C	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.1223A>G	12.37:g.56646642T>C	ENSP00000267116:p.His408Arg						p.H408R	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN			12	1344	-			408					A6NE79|B1Q2K2	Missense_Mutation	SNP	ENST00000267116.7	37	c.1223A>G	CCDS44920.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.193416	0.58017	.	.	ENSG00000139645	ENST00000267116;ENST00000417002	T	0.51817	0.69	4.28	4.28	0.50868	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.33469	0.0864	N	0.22421	0.69	0.80722	D	1	B	0.20780	0.048	B	0.13407	0.009	T	0.13522	-1.0506	10	0.39692	T	0.17	.	12.8717	0.57968	0.0:0.0:0.0:1.0	.	408	Q8NB46	ANR52_HUMAN	R	408	ENSP00000267116:H408R	ENSP00000267116:H408R	H	-	2	0	ANKRD52	54932909	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.791000	0.85805	1.944000	0.56390	0.533000	0.62120	CAT		0.522	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		13	19	0	0	0	1	0	13	19				
TIGD3	220359	broad.mit.edu	37	11	65123573	65123573	+	Silent	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr11:65123573G>A	ENST00000309880.5	+	2	501	c.294G>A	c.(292-294)acG>acA	p.T98T		NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	98	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						GGGACGTGACGGGGCCCATGC	0.642																																						ENST00000309880.5																			0				endometrium(3)|large_intestine(1)|lung(9)|prostate(2)|skin(2)	17						c.(292-294)acG>acA		tigger transposable element derived 3							59.0	63.0	62.0					11																	65123573		2201	4297	6498	SO:0001819	synonymous_variant	220359				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding	g.chr11:65123573G>A		CCDS8101.1	11q13.1	2008-07-21				ENSG00000173825			18334	protein-coding gene	gene with protein product							Standard	NM_145719		Approved		uc001odo.4	Q6B0B8		ENST00000309880.5:c.294G>A	11.37:g.65123573G>A							p.T98T	NM_145719.2	NP_663771.1	Q6B0B8	TIGD3_HUMAN			2	501	+			98			HTH CENPB-type.			Silent	SNP	ENST00000309880.5	37	c.294G>A	CCDS8101.1																																																																																				0.642	TIGD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387310.1	NM_145719		25	39	0	0	0	1	0	25	39				
REST	5978	broad.mit.edu	37	4	57777036	57777036	+	Missense_Mutation	SNP	C	C	T	rs142504829		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr4:57777036C>T	ENST00000309042.7	+	2	546	c.232C>T	c.(232-234)Ccg>Tcg	p.P78S		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	78	Interaction with SIN3A.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					AGAACTGATGCCGGTTGGGGA	0.448																																						ENST00000309042.7																			0				central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50						c.(232-234)Ccg>Tcg		RE1-silencing transcription factor		C	SER/PRO,SER/PRO	0,4406		0,0,2203	91.0	85.0	87.0		232,232	5.0	1.0	4	dbSNP_134	87	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	REST	NM_001193508.1,NM_005612.4	74,74	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	78/1098,78/1098	57777036	1,13005	2203	4300	6503	SO:0001583	missense	5978				cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding	g.chr4:57777036C>T	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.232C>T	4.37:g.57777036C>T	ENSP00000311816:p.Pro78Ser						p.P78S	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN			2	546	+	Glioma(25;0.08)|all_neural(26;0.181)		78			Interaction with SIN3A.		A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	c.232C>T	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.271228	0.80469	0.0	1.16E-4	ENSG00000084093	ENST00000456010;ENST00000309042;ENST00000358605	T	0.08984	3.03	5.92	5.0	0.66597	.	0.092113	0.45126	D	0.000389	T	0.13841	0.0335	L	0.44542	1.39	0.43555	D	0.995862	P;D	0.59357	0.905;0.985	P;P	0.58013	0.487;0.831	T	0.06144	-1.0843	10	0.10377	T	0.69	-14.9452	11.517	0.50526	0.3669:0.633:0.0:0.0	.	78;78	Q13127-2;Q13127	.;REST_HUMAN	S	78	ENSP00000311816:P78S	ENSP00000311816:P78S	P	+	1	0	REST	57471793	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.483000	0.73617	2.809000	0.96659	0.655000	0.94253	CCG		0.448	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		3	48	0	0	0	1	0	3	48				
CCSER1	401145	broad.mit.edu	37	4	91229784	91229784	+	Missense_Mutation	SNP	G	G	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr4:91229784G>T	ENST00000509176.1	+	2	637	c.349G>T	c.(349-351)Gtt>Ttt	p.V117F	CCSER1_ENST00000432775.2_Missense_Mutation_p.V117F|CCSER1_ENST00000333691.8_Missense_Mutation_p.V117F	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	117																	AAGACATTCTGTTGGTTTTAG	0.363																																						ENST00000509176.1																			0											c.(349-351)Gtt>Ttt		coiled-coil serine-rich protein 1							66.0	62.0	64.0					4																	91229784		1836	4094	5930	SO:0001583	missense	401145							g.chr4:91229784G>T		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.349G>T	4.37:g.91229784G>T	ENSP00000425040:p.Val117Phe					CCSER1_ENST00000333691.8_Missense_Mutation_p.V117F|CCSER1_ENST00000432775.2_Missense_Mutation_p.V117F	p.V117F	NM_001145065.1	NP_001138537.1					2	637	+								Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	c.349G>T	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.447247	0.43429	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.46819	1.36;0.86;1.36	5.18	5.18	0.71444	.	0.203324	0.42821	D	0.000654	T	0.35799	0.0944	L	0.27053	0.805	0.34356	D	0.690387	B;B;B	0.28350	0.183;0.112;0.208	B;B;B	0.30029	0.099;0.049;0.11	T	0.46596	-0.9180	10	0.35671	T	0.21	-9.4262	12.9117	0.58182	0.0754:0.0:0.9246:0.0	.	117;117;117	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	F	117	ENSP00000425040:V117F;ENSP00000389283:V117F;ENSP00000329482:V117F	ENSP00000329482:V117F	V	+	1	0	FAM190A	91448807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.335000	0.59298	2.793000	0.96121	0.655000	0.94253	GTT		0.363	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		3	46	1	0	1	1	1	3	46				
POLR1A	25885	broad.mit.edu	37	2	86258685	86258685	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr2:86258685C>T	ENST00000263857.6	-	30	4724	c.4346G>A	c.(4345-4347)cGa>cAa	p.R1449Q	POLR1A_ENST00000409681.1_Missense_Mutation_p.R1449Q			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1449					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						GTGGGGATTTCGTtcctcctg	0.577																																						ENST00000263857.6																			0				NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						c.(4345-4347)cGa>cAa		polymerase (RNA) I polypeptide A, 194kDa							171.0	172.0	172.0					2																	86258685		2138	4232	6370	SO:0001583	missense	25885				termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding	g.chr2:86258685C>T	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4346G>A	2.37:g.86258685C>T	ENSP00000263857:p.Arg1449Gln					POLR1A_ENST00000409681.1_Missense_Mutation_p.R1449Q	p.R1449Q			O95602	RPA1_HUMAN			30	4724	-			1449					B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	c.4346G>A	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409889	0.25465	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.65549	-0.16;3.29	4.39	1.54	0.23209	RNA polymerase Rpb1, domain 5 (1);	2.038040	0.01705	N	0.027407	T	0.37073	0.0990	N	0.02539	-0.55	0.09310	N	1	B	0.14805	0.011	B	0.06405	0.002	T	0.30208	-0.9986	10	0.16420	T	0.52	-11.3218	8.3032	0.32027	0.0:0.7161:0.0:0.2839	.	1449	O95602	RPA1_HUMAN	Q	1449	ENSP00000263857:R1449Q;ENSP00000386300:R1449Q	ENSP00000263857:R1449Q	R	-	2	0	POLR1A	86112196	0.013000	0.17824	0.149000	0.22428	0.023000	0.10783	0.126000	0.15769	0.565000	0.29255	0.555000	0.69702	CGA		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		22	31	0	0	0	1	0	22	31				
FHDC1	85462	broad.mit.edu	37	4	153897503	153897503	+	Silent	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr4:153897503G>A	ENST00000511601.1	+	12	3248	c.3060G>A	c.(3058-3060)ccG>ccA	p.P1020P	FHDC1_ENST00000260008.3_Silent_p.P1020P			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	1020									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CCAAGACCCCGTCAGTGCCCA	0.612																																						ENST00000511601.1																		ARFIP1/FHDC1(2)	0				NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43						c.(3058-3060)ccG>ccA		FH2 domain containing 1							61.0	71.0	68.0					4																	153897503		2203	4300	6503	SO:0001819	synonymous_variant	85462				actin cytoskeleton organization		actin binding	g.chr4:153897503G>A	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.3060G>A	4.37:g.153897503G>A						FHDC1_ENST00000260008.3_Silent_p.P1020P	p.P1020P			Q9C0D6	FHDC1_HUMAN			12	3248	+	all_hematologic(180;0.093)		1020						Silent	SNP	ENST00000511601.1	37	c.3060G>A	CCDS34081.1																																																																																				0.612	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		5	54	0	0	0	1	0	5	54				
MATN4	8785	broad.mit.edu	37	20	43929859	43929859	+	Missense_Mutation	SNP	C	C	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr20:43929859C>A	ENST00000372754.1	-	5	903	c.895G>T	c.(895-897)Gac>Tac	p.D299Y	MATN4_ENST00000342716.4_Missense_Mutation_p.D258Y|MATN4_ENST00000353917.5_Intron|MATN4_ENST00000360607.6_Missense_Mutation_p.D217Y|MATN4_ENST00000537548.1_Missense_Mutation_p.D258Y|MATN4_ENST00000372751.4_Missense_Mutation_p.D109Y|MATN4_ENST00000372756.1_Missense_Mutation_p.D258Y			O95460	MATN4_HUMAN	matrilin 4	299	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CTGCAGTAGTCAATGGCTGGC	0.592											OREG0025977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000537548.1																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						c.(772-774)Gac>Tac		matrilin 4							82.0	84.0	84.0					20																	43929859		2203	4300	6503	SO:0001583	missense	8785					extracellular region	protein binding	g.chr20:43929859C>A	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.895G>T	20.37:g.43929859C>A	ENSP00000361840:p.Asp299Tyr		OREG0025977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	920	MATN4_ENST00000372754.1_Missense_Mutation_p.D299Y|MATN4_ENST00000372756.1_Missense_Mutation_p.D258Y|MATN4_ENST00000353917.5_Intron|MATN4_ENST00000342716.4_Missense_Mutation_p.D258Y|MATN4_ENST00000372753.1_Missense_Mutation_p.D109Y|MATN4_ENST00000372751.4_Missense_Mutation_p.D109Y|MATN4_ENST00000360607.5_Missense_Mutation_p.D217Y	p.D258Y			O95460	MATN4_HUMAN			6	1016	-		Myeloproliferative disorder(115;0.0122)	299			EGF-like 2.		A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	37	c.772G>T		.	.	.	.	.	.	.	.	.	.	C	20.2	3.945707	0.73672	.	.	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	D;D;D;T;D;D;D	0.97209	-2.41;-2.41;-4.29;-0.52;-4.29;-4.29;-2.41	5.25	4.31	0.51392	.	0.145914	0.31358	N	0.007799	D	0.98940	0.9640	H	0.97265	3.97	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.75484	0.971;0.986	D	0.99191	1.0870	10	0.87932	D	0	.	13.0623	0.59014	0.0:0.9235:0.0:0.0765	.	217;258	O95460-4;O95460-2	.;.	Y	109;299;258;217;258;258;299;109	ENSP00000361839:D109Y;ENSP00000361840:D299Y;ENSP00000361842:D258Y;ENSP00000353819:D217Y;ENSP00000343164:D258Y;ENSP00000440328:D258Y;ENSP00000361837:D109Y	ENSP00000255132:D299Y	D	-	1	0	MATN4	43363273	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	2.318000	0.43779	1.464000	0.47987	0.650000	0.86243	GAC		0.592	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			4	86	1	0	0.00024832	1	0.000260145	4	86				
PAX4	5078	broad.mit.edu	37	7	127255484	127255484	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr7:127255484G>A	ENST00000341640.2	-	1	296	c.91C>T	c.(91-93)Cgg>Tgg	p.R31W	PAX4_ENST00000378740.2_Missense_Mutation_p.R31W|PAX4_ENST00000338516.3_Missense_Mutation_p.R39W|PAX4_ENST00000463946.1_5'UTR	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	39	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.R31W(1)		cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						TCACAGGGCCGCATTCCACTG	0.582																																					Ovarian(113;737 1605 7858 27720 34092)	ENST00000341640.2																			1	Substitution - Missense(1)	p.R31W(1)	cervix(1)	cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						c.(91-93)Cgg>Tgg		paired box 4							94.0	95.0	95.0					7																	127255484		2203	4300	6503	SO:0001583	missense	5078				cell differentiation|endocrine pancreas development|organ morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:127255484G>A		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"""Paired boxes"", ""Homeoboxes / PRD class"""	8618	protein-coding gene	gene with protein product		167413	"""paired box gene 4"""				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.91C>T	7.37:g.127255484G>A	ENSP00000339906:p.Arg31Trp					PAX4_ENST00000338516.3_Missense_Mutation_p.R39W|PAX4_ENST00000463946.1_5'UTR|PAX4_ENST00000378740.2_Missense_Mutation_p.R31W	p.R31W	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN			1	296	-			39			Paired.		O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	c.91C>T	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	G	32	5.148510	0.94603	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740	D;D	0.99680	-6.38;-6.38	5.73	5.73	0.89815	Paired box protein, N-terminal (5);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99768	0.9905	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97395	0.9992	10	0.87932	D	0	.	17.4002	0.87458	0.0:0.0:1.0:0.0	.	31;39	O43316-4;O43316	.;PAX4_HUMAN	W	31;39;39	ENSP00000339906:R31W;ENSP00000344297:R39W	ENSP00000344297:R39W	R	-	1	2	PAX4	127042720	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.065000	0.49994	2.693000	0.91896	0.655000	0.94253	CGG		0.582	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			3	73	0	0	0	1	0	3	73				
LEF1	51176	broad.mit.edu	37	4	109000748	109000748	+	Missense_Mutation	SNP	C	C	T	rs146861754		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr4:109000748C>T	ENST00000265165.1	-	7	1399	c.745G>A	c.(745-747)Ggt>Agt	p.G249S	LEF1_ENST00000510624.1_Missense_Mutation_p.G153S|LEF1_ENST00000438313.2_Missense_Mutation_p.G221S|LEF1_ENST00000503879.1_5'Flank|LEF1_ENST00000379951.2_Missense_Mutation_p.G221S	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	249	Pro-rich.				alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G249S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		CCAGGAGGACCGGGAATCATA	0.468																																						ENST00000379951.2																			1	Substitution - Missense(1)	p.G249S(1)	large_intestine(1)	endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25						c.(661-663)Ggt>Agt		lymphoid enhancer-binding factor 1		C	SER/GLY,SER/GLY,SER/GLY,SER/GLY	1,4405	2.1+/-5.4	0,1,2202	208.0	179.0	189.0		661,661,457,745	5.8	1.0	4	dbSNP_134	189	0,8600		0,0,4300	no	missense,missense,missense,missense	LEF1	NM_001130713.2,NM_001130714.2,NM_001166119.1,NM_016269.4	56,56,56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	221/372,221/387,153/304,249/400	109000748	1,13005	2203	4300	6503	SO:0001583	missense	51176				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding	g.chr4:109000748C>T		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.745G>A	4.37:g.109000748C>T	ENSP00000265165:p.Gly249Ser					LEF1_ENST00000438313.2_Missense_Mutation_p.G221S|LEF1_ENST00000510624.1_Missense_Mutation_p.G153S|LEF1_ENST00000265165.1_Missense_Mutation_p.G249S	p.G221S	NM_001130713.2|NM_001130714.2	NP_001124185.1|NP_001124186.1	Q9UJU2	LEF1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000224)	6	1849	-			249			Pro-rich.		B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Missense_Mutation	SNP	ENST00000265165.1	37	c.661G>A	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275864	0.80580	2.27E-4	0.0	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624	D;D;D;D	0.99194	-5.38;-5.46;-5.48;-5.54	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.97726	0.9254	N	0.05306	-0.075	0.80722	D	1	D;D;D;P;B	0.89917	1.0;1.0;1.0;0.758;0.238	D;D;D;B;B	0.91635	0.987;0.991;0.999;0.249;0.079	D	0.94608	0.7802	10	0.06099	T	0.92	0.2914	20.1731	0.98165	0.0:1.0:0.0:0.0	.	153;106;221;221;249	E9PDK3;B4DZY5;Q9UJU2-6;Q9UJU2-5;Q9UJU2	.;.;.;.;LEF1_HUMAN	S	249;221;221;153	ENSP00000265165:G249S;ENSP00000369284:G221S;ENSP00000406176:G221S;ENSP00000422840:G153S	ENSP00000265165:G249S	G	-	1	0	LEF1	109220197	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.817000	0.62650	2.768000	0.95171	0.655000	0.94253	GGT		0.468	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			3	44	0	0	0	1	0	3	44				
ISLR	3671	broad.mit.edu	37	15	74468241	74468241	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr15:74468241G>A	ENST00000249842.3	+	2	1399	c.1042G>A	c.(1042-1044)Ggt>Agt	p.G348S	ISLR_ENST00000395118.1_Missense_Mutation_p.G348S|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	348					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						GGCCACGCCCGGTGAGGGTGG	0.632																																						ENST00000249842.3																			0				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						c.(1042-1044)Ggt>Agt		immunoglobulin superfamily containing leucine-rich repeat							71.0	61.0	64.0					15																	74468241		2198	4297	6495	SO:0001583	missense	3671				cell adhesion	extracellular region		g.chr15:74468241G>A	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.1042G>A	15.37:g.74468241G>A	ENSP00000249842:p.Gly348Ser					ISLR_ENST00000395118.1_Missense_Mutation_p.G348S|RP11-665J16.1_ENST00000561647.1_RNA	p.G348S	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN			2	1399	+			348						Missense_Mutation	SNP	ENST00000249842.3	37	c.1042G>A	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	6.727	0.502813	0.12822	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.60797	0.16;0.16	4.34	3.42	0.39159	.	0.214388	0.24737	U	0.036002	T	0.30603	0.0770	N	0.14661	0.345	0.09310	N	1	P	0.43633	0.813	B	0.33620	0.167	T	0.12344	-1.0551	10	0.15952	T	0.53	.	8.602	0.33751	0.1772:0.0:0.8228:0.0	.	348	O14498	ISLR_HUMAN	S	348	ENSP00000249842:G348S;ENSP00000378550:G348S	ENSP00000249842:G348S	G	+	1	0	ISLR	72255294	0.060000	0.20803	0.003000	0.11579	0.001000	0.01503	0.923000	0.28757	0.820000	0.34516	-0.339000	0.08088	GGT		0.632	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		8	15	0	0	0	1	0	8	15				
POM121L9P	29774	broad.mit.edu	37	22	24659591	24659591	+	RNA	SNP	A	A	G			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr22:24659591A>G	ENST00000414583.2	+	0	3116					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		ACTCACTGACATCGAAGGCTG	0.632																																						ENST00000414583.2																			0																																																			0							g.chr22:24659591A>G	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659591A>G								NR_003714.1						0	3116	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	13	0	0	0	1	0	3	13				
CDH23	64072	broad.mit.edu	37	10	73437354	73437354	+	Missense_Mutation	SNP	G	G	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr10:73437354G>T	ENST00000224721.6	+	15	1676	c.1671G>T	c.(1669-1671)ttG>ttT	p.L557F	CDH23_ENST00000299366.7_Missense_Mutation_p.L597F	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	552	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TCAATGTGTTGGATGTCAACG	0.617																																						ENST00000224721.6																			0				NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						c.(1669-1671)ttG>ttT		cadherin-related 23							40.0	44.0	43.0					10																	73437354		2131	4240	6371	SO:0001583	missense	64072				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding	g.chr10:73437354G>T	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1671G>T	10.37:g.73437354G>T	ENSP00000224721:p.Leu557Phe					CDH23_ENST00000299366.7_Missense_Mutation_p.L597F	p.L557F	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN			15	1676	+			552			Cadherin 5.		C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37	c.1671G>T		.	.	.	.	.	.	.	.	.	.	G	17.72	3.458569	0.63401	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.49	0.472	0.16758	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.53938	D	0.000053	T	0.61714	0.2369	L	0.46614	1.455	0.80722	D	1	D;D;P	0.56746	0.963;0.977;0.727	D;P;P	0.65573	0.936;0.79;0.489	T	0.57136	-0.7863	9	0.52906	T	0.07	.	6.9766	0.24679	0.3163:0.1088:0.5749:0.0	.	552;555;552	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	F	557;552;552;555;555;69	.	ENSP00000224721:L557F	L	+	3	2	CDH23	73107360	1.000000	0.71417	0.898000	0.35279	0.690000	0.40134	0.547000	0.23299	-0.156000	0.11079	-0.266000	0.10368	TTG		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		9	7	1	0	2.17888e-05	1	2.33831e-05	9	7				
LOC645752	645752	broad.mit.edu	37	15	78211648	78211648	+	lincRNA	SNP	A	A	G	rs577974396	byFrequency	TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr15:78211648A>G	ENST00000565869.1	+	0	111				RN7SL214P_ENST00000487317.2_RNA|RP11-114H24.2_ENST00000567226.1_RNA																							CGCCAGGGATAGGGGCTCAGC	0.522																																						ENST00000565869.1																			0																																																			0							g.chr15:78211648A>G																													15.37:g.78211648A>G						RP11-114H24.2_ENST00000567226.1_RNA								0	111	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.522	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			4	60	0	0	0	1	0	4	60				
AGPS	8540	broad.mit.edu	37	2	178386036	178386036	+	Silent	SNP	C	C	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr2:178386036C>T	ENST00000264167.4	+	18	1883	c.1737C>T	c.(1735-1737)ttC>ttT	p.F579F	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	579					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			GTATCTACTTCTATTTTGCCT	0.388																																						ENST00000264167.4																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32						c.(1735-1737)ttC>ttT		alkylglycerone phosphate synthase							176.0	165.0	169.0					2																	178386036		2203	4300	6503	SO:0001819	synonymous_variant	8540				ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity	g.chr2:178386036C>T	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1737C>T	2.37:g.178386036C>T						AGPS_ENST00000409888.1_Intron	p.F579F	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)		18	1883	+			579					A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	c.1737C>T	CCDS2275.1																																																																																				0.388	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			33	75	0	0	0	1	0	33	75				
PPFIA3	8541	broad.mit.edu	37	19	49636536	49636536	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr19:49636536G>A	ENST00000334186.4	+	9	1418	c.1069G>A	c.(1069-1071)Gcc>Acc	p.A357T	PPFIA3_ENST00000602351.1_Missense_Mutation_p.A357T	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	357					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GTTGGACGACGCCAAGCAGAA	0.687																																						ENST00000334186.4																			0				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35						c.(1069-1071)Gcc>Acc		protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3							29.0	32.0	31.0					19																	49636536		2198	4292	6490	SO:0001583	missense	8541					cell surface|cytoplasm	protein binding	g.chr19:49636536G>A	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"""Sterile alpha motif (SAM) domain containing"""	9247	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3"", ""liprin-alpha 3"", ""liprin"""	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.1069G>A	19.37:g.49636536G>A	ENSP00000335614:p.Ala357Thr					PPFIA3_ENST00000602351.1_Missense_Mutation_p.A357T	p.A357T	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)	9	1418	+		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)	357					A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	37	c.1069G>A	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224238	0.79576	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.21734	1.99	3.91	3.91	0.45181	.	0.130592	0.31760	N	0.007106	T	0.43233	0.1238	M	0.85197	2.74	0.58432	D	0.999995	D;D;B	0.58620	0.983;0.972;0.026	P;P;B	0.54924	0.718;0.764;0.04	T	0.54029	-0.8354	10	0.56958	D	0.05	-8.6564	15.2619	0.73631	0.0:0.0:1.0:0.0	.	281;357;357	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	T	357;281	ENSP00000335614:A357T	ENSP00000335614:A357T	A	+	1	0	PPFIA3	54328348	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	9.507000	0.97996	2.213000	0.71641	0.555000	0.69702	GCC		0.687	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		4	40	0	0	0	1	0	4	40				
KRTAP5-5	439915	broad.mit.edu	37	11	1651241	1651241	+	Silent	SNP	A	A	C			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr11:1651241A>C	ENST00000399676.2	+	1	209	c.171A>C	c.(169-171)ggA>ggC	p.G57G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	57						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gctgtgggggatgtggctccg	0.682																																						ENST00000399676.2																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33						c.(169-171)ggA>ggC		keratin associated protein 5-5							47.0	59.0	55.0					11																	1651241		2188	4272	6460	SO:0001819	synonymous_variant	439915					keratin filament		g.chr11:1651241A>C	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.171A>C	11.37:g.1651241A>C							p.G57G	NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	1	209	+		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	57					A8MWN2	Silent	SNP	ENST00000399676.2	37	c.171A>C	CCDS41592.1																																																																																				0.682	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			4	77	0	0	0	1	0	4	77				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000564451.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000567960.1_RNA								0	1866	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		3	59	0	0	0	1	0	3	59				
KRT85	3891	broad.mit.edu	37	12	52761081	52761081	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr12:52761081C>T	ENST00000257901.3	-	1	184	c.109G>A	c.(109-111)Gcc>Acc	p.A37T	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	37	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CGGTAGGGGGCGGCGCTGATG	0.672																																						ENST00000257901.3																			0				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36						c.(109-111)Gcc>Acc		keratin 85							22.0	25.0	24.0					12																	52761081		2203	4300	6503	SO:0001583	missense	3891				epidermis development	keratin filament	protein binding|structural molecule activity	g.chr12:52761081C>T	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.109G>A	12.37:g.52761081C>T	ENSP00000257901:p.Ala37Thr						p.A37T	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.189)	1	184	-	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)		37			Head.		Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	c.109G>A	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.532821	0.27387	.	.	ENSG00000135443	ENST00000257901	D	0.81739	-1.53	4.74	2.92	0.33932	.	0.112267	0.40469	N	0.001099	T	0.69387	0.3105	L	0.43701	1.375	0.09310	N	0.999994	B	0.12630	0.006	B	0.09377	0.004	T	0.55289	-0.8164	10	0.30078	T	0.28	.	7.2335	0.26057	0.0:0.6659:0.1331:0.201	.	37	P78386	KRT85_HUMAN	T	37	ENSP00000257901:A37T	ENSP00000257901:A37T	A	-	1	0	KRT85	51047348	0.010000	0.17322	0.591000	0.28745	0.695000	0.40330	0.307000	0.19296	0.721000	0.32231	-0.264000	0.10439	GCC		0.672	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		3	24	0	0	0	1	0	3	24				
HSP90AA1	3320	broad.mit.edu	37	14	102548543	102548543	+	Nonsense_Mutation	SNP	A	A	T			TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr14:102548543A>T	ENST00000216281.8	-	10	2199	c.1994T>A	c.(1993-1995)tTg>tAg	p.L665*	HSP90AA1_ENST00000334701.7_Nonsense_Mutation_p.L787*	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	665					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	TTCATAAAGCAAGATGACCAG	0.458																																						ENST00000334701.7																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28						c.(2359-2361)tTg>tAg		heat shock protein 90kDa alpha (cytosolic), class A member 1	Rifabutin(DB00615)						123.0	117.0	119.0					14																	102548543		2203	4300	6503	SO:0001587	stop_gained	3320				axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding	g.chr14:102548543A>T	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.1994T>A	14.37:g.102548543A>T	ENSP00000216281:p.Leu665*					HSP90AA1_ENST00000216281.8_Nonsense_Mutation_p.L665*	p.L787*	NM_001017963.2	NP_001017963.2	P07900	HS90A_HUMAN			11	2641	-			665					A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Nonsense_Mutation	SNP	ENST00000216281.8	37	c.2360T>A	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	a	41	8.886985	0.98990	.	.	ENSG00000080824	ENST00000216281;ENST00000334701	.	.	.	4.47	4.47	0.54385	.	0.000000	0.64402	U	0.000008	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6149	14.1096	0.65113	1.0:0.0:0.0:0.0	.	.	.	.	X	665;787	.	ENSP00000216281:L665X	L	-	2	0	HSP90AA1	101618296	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	1.805000	0.52779	0.473000	0.43528	TTG		0.458	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		42	115	0	0	0	1	0	42	115				
DUSP27	92235	broad.mit.edu	37	1	167095398	167095400	+	In_Frame_Del	DEL	GAG	GAG	-	rs372437301		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr1:167095398_167095400delGAG	ENST00000361200.2	+	6	1196_1198	c.1030_1032delGAG	c.(1030-1032)gagdel	p.E348del	DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000443333.1_In_Frame_Del_p.E348del|DUSP27_ENST00000271385.5_In_Frame_Del_p.E348del			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	348					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CCTCATAGACGAGGAGGAGGAGG	0.655																																						ENST00000361200.2																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						c.(1030-1032)del		dual specificity phosphatase 27 (putative)				121,4133		6,109,2012						-6.5	0.0			29	285,7951		13,259,3846	no	coding	DUSP27	NM_001080426.1		19,368,5858	A1A1,A1R,RR		3.4604,2.8444,3.2506				406,12084				SO:0001651	inframe_deletion	92235				protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity	g.chr1:167095398_167095400delGAG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1030_1032delGAG	1.37:g.167095407_167095409delGAG	ENSP00000354483:p.Glu348del					DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_In_Frame_Del_p.E348del|DUSP27_ENST00000443333.1_In_Frame_Del_p.E348del	p.E348del			Q5VZP5	DUS27_HUMAN			6	1196_1198	+			348					A0AUM4|Q9C074	In_Frame_Del	DEL	ENST00000361200.2	37	c.1030_1032delGAG	CCDS30932.1																																																																																				0.655	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		3	6						3	6	---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78790207	78790208	+	Intron	INS	-	-	GAATA	rs55947300|rs10124596|rs71372053	byFrequency	TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr9:78790207_78790208insGAATA	ENST00000545128.1	+	14	2438				PCSK5_ENST00000376767.3_Frame_Shift_Ins_p.-689fs|PCSK5_ENST00000376752.4_Intron	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						cgaatcgaatcgaatagaatag	0.342																																						ENST00000376767.3																			0				NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						c.(2062-2064)aatfs		proprotein convertase subtilisin/kexin type 5																																				SO:0001627	intron_variant	5125				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity	g.chr9:78790207_78790208insGAATA		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1900+162->GAATA	9.37:g.78790213_78790217dupGAATA						PCSK5_ENST00000376752.4_Intron|PCSK5_ENST00000545128.1_Intron	p.N688fs			Q92824	PCSK5_HUMAN			14	2574_2575	+			0			CRM (Cys-rich motif).		F5H2G7|Q13527|Q96EP4	Frame_Shift_Ins	INS	ENST00000545128.1	37	c.2062_2063insGAATA	CCDS55320.1																																																																																				0.342	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				2	4						2	4	---	---	---	---
SNHG24	101929369	broad.mit.edu	37	14	101440134	101440137	+	lincRNA	DEL	AATA	AATA	-	rs531110242		TCGA-KK-A8I8-01A-11D-A364-08	TCGA-KK-A8I8-11A-11D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99d7021e-f0da-44fb-8f6c-5bcd2c433a0e	fe39a0c2-56d9-445c-ab4b-744d4d21f8c2	g.chr14:101440134_101440137delAATA	ENST00000554693.2	+	0	384				SNORD114-19_ENST00000363072.1_RNA|SNORD114-15_ENST00000364687.1_RNA|SNORD114-16_ENST00000363044.1_RNA|SNORD114-14_ENST00000362723.1_RNA|SNORD114-18_ENST00000365272.1_RNA|SNORD114-17_ENST00000364699.1_RNA																							TCAAGGGCAGaataaataaattta	0.279																																						ENST00000554693.2																			0																																																			0							g.chr14:101440134_101440137delAATA																													14.37:g.101440138_101440141delAATA														0	384	+									RNA	DEL	ENST00000554693.2	37																																																																																						0.279	RP11-909M7.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000468646.1			4	5						4	5	---	---	---	---
