#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_CCF_CI95_high	i_CCF_CI95_low	i_CCF_CI_high	i_CCF_CI_low	i_CCF_hat	i_CCF_mean	i_CCF_median	i_CCF_mode	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_CancerGermlineMut	i_CGC_CancerMolecularGenetics	i_CGC_CancerSomaticMut	i_CGC_CancerSyndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_ChrBand	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_OtherGermlineMut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_TissueType	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_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_ExAC_AC	i_ExAC_AN	i_ExAC_LQ	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_IS_SCNA	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_SCNA_NA	i_SCNA_NB	i_SCNA_q_hat	i_SCNA_tau	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_bcgsc	i_broad	i_build	i_cDNA_Change	i_ccds_id	i_clonal	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_dna_fraction_in_tumor	i_entrez_gene_id	i_external_id_capture	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_hgsc	i_igv_bad	i_localAssembly_detected	i_min_val_count_KRAS	i_min_val_count_localAssembly	i_min_val_count_rna	i_min_val_count_targeted	i_n_alt_count	i_n_alt_count_KRAS	i_n_alt_count_full	i_n_alt_count_localAssembly	i_n_ref_count	i_n_ref_count_KRAS	i_n_ref_count_full	i_n_ref_count_localAssembly	i_passExAC	i_ploidy	i_pon_loglike	i_pon_pass_loglike	i_purity	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_KRAS	i_t_alt_count_full	i_t_alt_count_localAssembly	i_t_ref_count_KRAS	i_t_ref_count_full	i_t_ref_count_localAssembly	i_ucsc	i_validation_judgement_KRAS	i_validation_judgement_localAssembly	i_validation_judgement_rna	i_validation_judgement_targeted	i_validation_normal_alt_count_rna	i_validation_normal_alt_count_targeted	i_validation_normal_ref_count_rna	i_validation_normal_ref_count_targeted	i_validation_power_KRAS	i_validation_power_localAssembly	i_validation_power_rna	i_validation_power_targeted	i_validation_tumor_alt_count_rna	i_validation_tumor_alt_count_targeted	i_validation_tumor_ref_count_rna	i_validation_tumor_ref_count_targeted	t_alt_count	t_ref_count
SMYD3	64754	broad.mit.edu	37	1	246078893	246078893	+	Frame_Shift_Del	DEL	T	T	-			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			T	-	T	T		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr1:246078893delT	ENST00000388985.4	-	8	751	c.752delA	c.(751-753)aagfs	p.K251fs	SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Frame_Shift_Del_p.K192fs|SMYD3_ENST00000490107.1_Frame_Shift_Del_p.K192fs			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	251					cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CCTCAGCTGCTTCCGGCGCTC	0.527																																						ENST00000388985.4	0.750000	4.800000e-01	6.800000e-01	5.400000e-01	0.600000	0.613556	0.600000	0.610000																										0				17						c.(751-753)aagfs		SET and MYND domain containing 3							123.0	100.0	108.0					1																	246078893		2203	4300	6503	SO:0001589	frameshift_variant	64754	0	0					g.chr1:246078893delT	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	15513	protein-coding gene	gene with protein product		608783	"""zinc finger, MYND domain containing 1"""	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.752delA	chr1.hg19:g.246078893delT	ENSP00000373637:p.Lys251fs	0					SMYD3_ENST00000541742.1_Frame_Shift_Del_p.K192fs|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000490107.1_Frame_Shift_Del_p.K192fs	p.K251fs			1	2	3	2.124265	Q9H7B4	SMYD3_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	8	751	-	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Frame_Shift_Del	DEL	ENST00000388985.4	1	1	hg19	c.752delA	CCDS53486.1	0																																																																																								0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.527	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		1	0	1		2	2		0		0	0	97		97	95	1	1.830000	-20.000000	1	0.520000	NM_022743			78	88		420	415	0		1	0	0	0	0	97	0		1.000000	9.969400e-01	0	0	0	49	0	78	420
RBP3	5949	broad.mit.edu	37	10	48389752	48389752	+	Silent	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr10:48389752G>A	ENST00000224600.4	-	1	1239	c.1126C>T	c.(1126-1128)Ctg>Ttg	p.L376L	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	376	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GCAGCCTGCAGGCCGGCATTG	0.652																																						ENST00000224600.4	1.000000	6.500000e-01	9.700000e-01	7.400000e-01	0.840000	0.851735	0.840000	1.000000																										0				59						c.(1126-1128)Ctg>Ttg		retinol binding protein 3, interstitial	Vitamin A(DB00162)						33.0	36.0	35.0					10																	48389752		2201	4300	6501	SO:0001819	synonymous_variant	5949	0	0					g.chr10:48389752G>A	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.1126C>T	chr10.hg19:g.48389752G>A		0					AL731561.2_ENST00000581861.1_RNA	p.L376L	NM_002900.2	NP_002891.1	1	2	3	2.134617	P10745	RET3_HUMAN		1	1239	-			Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	1	1	hg19	c.1126C>T	CCDS7218.1	0																																																																																								0.524941		TCGA-2J-AABU-01A-11D-A40W-08	0.652	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	1	0	1		2	2	2	0		0	0	46		46	45	1	1.830000	-20.000000	1	0.520000	NM_002900			52	52		187	184	1		1			0	0	46	0		1.000000	0	0	0	0	0	0	52	187
SF3B2	10992	broad.mit.edu	37	11	65826742	65826742	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr11:65826742C>T	ENST00000322535.6	+	11	1302	c.1253C>T	c.(1252-1254)gCc>gTc	p.A418V	SF3B2_ENST00000528302.1_Missense_Mutation_p.A401V	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	418					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AACTCTGCAGCCCCCAAGAAG	0.532																																						ENST00000322535.6	1.000000	5.600000e-01	9.700000e-01	6.800000e-01	0.810000	0.821772	0.810000	1.000000																										0				41						c.(1252-1254)gCc>gTc		splicing factor 3b, subunit 2, 145kDa							62.0	55.0	58.0					11																	65826742		2201	4295	6496	SO:0001583	missense	10992	0	0					g.chr11:65826742C>T	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1253C>T	chr11.hg19:g.65826742C>T	ENSP00000318861:p.Ala418Val	0					SF3B2_ENST00000528302.1_Missense_Mutation_p.A401V	p.A418V	NM_006842.2	NP_006833.2	1	2	3	2.120231	Q13435	SF3B2_HUMAN		11	1302	+			A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	1	1	hg19	c.1253C>T	CCDS31612.1	0	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315405	0.23908	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.06	-0.939	0.10408	5.06	-0.939	0.10408	.	0.379232	0.29073	N	0.013223	T	0.23289	0.0563	L	0.27053	0.805	0.19575	N	0.999966	B	0.02656	0.0	B	0.04013	0.001	T	0.20140	-1.0284	9	0.18276	T	0.48	0.0053	8.4596	0.32921	0.0:0.4852:0.0:0.5148	.	418	Q13435	SF3B2_HUMAN	V	401;418;322	.	ENSP00000318861:A418V	A	+	2	0	0	SF3B2	65583318	65583318	0.339000	0.24784	0.028000	0.17463	0.984000	0.73092	0.269000	0.18589	-0.516000	0.06470	0.555000	0.69702	GCC	0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.532	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2	1	0	1		2	2	2	0		0	0	24		24	24	1	1.830000	-18.327550	1	0.520000				26	24		97	94	1		1	1		0	0	24	0		1.000000	1	0	56	0	106	0	26	97
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	G	rs121913530		TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr12:25398285C>G	ENST00000256078.4	-	2	97	c.34G>C	c.(34-36)Ggt>Cgt	p.G12R	KRAS_ENST00000311936.3_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000556131.1_Missense_Mutation_p.G12R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	ENST00000256078.4	1.000000	9.900000e-01	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119		Dom	yes			Dom	yes		12	12p12.1	12p12.1	3845	Mis	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog				"""L, E, M, O"""	L, E, M, O			pancreatic, colorectal, lung, thyroid, AML, others	UBE2L3/KRAS(2)	5144	Substitution - Missense(5142)|Insertion - In frame(2)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	25349	GRCh37	CM076251	KRAS	M	rs121913530	c.(34-36)Ggt>Cgt		Kirsten rat sarcoma viral oncogene homolog							93.0	83.0	86.0					12																	25398285		2203	4300	6503	SO:0001583	missense	3845	0	0		Noonan syndrome;Cardiofaciocutaneous syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	g.chr12:25398285C>G	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>C	chr12.hg19:g.25398285C>G	ENSP00000256078:p.Gly12Arg	1	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R	p.G12R	NM_033360.2	NP_203524.1	1	3	4	2.973774	P01116	RASK_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)	2	97	-	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	1	1	hg19	c.34G>C	CCDS8703.1	1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930538	0.92389	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.68	5.68	0.88126	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84893	0.5573	M	0.84082	2.675	0.80722	D	1	P;P	0.43287	0.802;0.741	B;P	0.47941	0.36;0.562	D	0.86658	0.1902	10	0.66056	D	0.02	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	R	12	ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R	ENSP00000256078:G12R	G	-	1	0	0	KRAS	25289552	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	0.655963		TCGA-2J-AABU-01A-11D-A40W-08	0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1		2	2	2	0		0	0	84		84	82	1	1.830000	-20.000000	1	0.520000	NM_033360			80	80		146	145	1		1	1	1	0	0	84	272		1.000000	9.570018e-01	1	5	84	7	180	80	146
KCNH3	23416	broad.mit.edu	37	12	49943305	49943305	+	Missense_Mutation	SNP	G	G	A	rs201995852		TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr12:49943305G>A	ENST00000257981.6	+	9	1810	c.1550G>A	c.(1549-1551)cGc>cAc	p.R517H		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	517					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						TACCACAGCCGCACGCGCGAC	0.637																																						ENST00000257981.6	1.000000	8.700000e-01	1	9.500000e-01	0.990000	0.983093	0.990000	1.000000																										0				36						c.(1549-1551)cGc>cAc		potassium voltage-gated channel, subfamily H (eag-related), member 3							81.0	70.0	74.0					12																	49943305		2203	4300	6503	SO:0001583	missense	23416	2	121400	32				g.chr12:49943305G>A	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1550G>A	chr12.hg19:g.49943305G>A	ENSP00000257981:p.Arg517His	1						p.R517H	NM_012284.1	NP_036416.1	0	1	1	1.727803	Q9ULD8	KCNH3_HUMAN		9	1810	+			Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	1	1	hg19	c.1550G>A	CCDS8786.1	1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976805	0.92982	.	.	ENSG00000135519	ENST00000257981	D	0.96802	-4.13	4.89	4.0	0.46444	4.89	4.0	0.46444	Cyclic nucleotide-binding-like (1);	0.136777	0.34460	N	0.003957	D	0.93406	0.7897	M	0.65320	2	0.44073	D	0.996821	P	0.51791	0.948	B	0.36186	0.219	D	0.92864	0.6308	10	0.72032	D	0.01	.	11.3196	0.49412	0.0892:0.0:0.9108:0.0	.	517	Q9ULD8	KCNH3_HUMAN	H	517	ENSP00000257981:R517H	ENSP00000257981:R517H	R	+	2	0	0	KCNH3	48229572	48229572	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.599000	0.74127	1.441000	0.47550	-0.140000	0.14226	CGC	0.366922		TCGA-2J-AABU-01A-11D-A40W-08	0.637	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	1	0	1		2	2	2	0		0	0	77		77	60	1	1.830000	-20.000000	1	0.520000	NM_012284			80	54		130	87	1		1			0	0	77	0		1.000000	0	0	0	0	0	0	80	130
LUM	4060	broad.mit.edu	37	12	91502249	91502249	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr12:91502249G>A	ENST00000266718.4	-	2	962	c.508C>T	c.(508-510)Cgg>Tgg	p.R170W	LUM_ENST00000548071.1_Intron	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	170					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.R170R(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						TCTTTCAGCCGATTGTGCTGG	0.443																																						ENST00000266718.4	1.000000	8.700000e-01	1	9.400000e-01	0.990000	0.980157	0.990000	1.000000																										1	Substitution - coding silent(1)	p.R170R(1)	large_intestine(1)	24						c.(508-510)Cgg>Tgg		lumican							98.0	100.0	99.0					12																	91502249		2203	4300	6503	SO:0001583	missense	4060	1	121412	28				g.chr12:91502249G>A	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6724	protein-coding gene	gene with protein product	"""lumican proteoglycan"""	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.508C>T	chr12.hg19:g.91502249G>A	ENSP00000266718:p.Arg170Trp	1					LUM_ENST00000548071.1_Intron	p.R170W	NM_002345.3	NP_002336.1	0	1	1	1.727803	P51884	LUM_HUMAN		2	962	-			B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	1	1	hg19	c.508C>T	CCDS9038.1	1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.841053	0.32513	.	.	ENSG00000139329	ENST00000266718	T	0.58652	0.32	5.6	5.6	0.85130	5.6	5.6	0.85130	.	0.355674	0.30329	N	0.009863	T	0.64583	0.2611	L	0.49699	1.58	0.26729	N	0.970633	P	0.49090	0.919	P	0.53062	0.717	T	0.61831	-0.6982	10	0.59425	D	0.04	-14.9632	15.1305	0.72520	0.0:0.1408:0.8592:0.0	.	170	P51884	LUM_HUMAN	W	170	ENSP00000266718:R170W	ENSP00000266718:R170W	R	-	1	2	2	LUM	90026380	90026380	1.000000	0.71417	0.998000	0.56505	0.555000	0.35460	2.608000	0.46308	2.648000	0.89879	0.557000	0.71058	CGG	0.366922		TCGA-2J-AABU-01A-11D-A40W-08	0.443	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	1	0	1		2	2	2	0		0	0	129		129	129	1	1.830000	-13.406100	1	0.520000	NM_002345			103	101		180	179	1		1	1		0	0	129	0		1.000000	1	0	10	0	708	0	103	180
NYNRIN	57523	broad.mit.edu	37	14	24886612	24886612	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr14:24886612A>G	ENST00000382554.3	+	9	5975	c.5657A>G	c.(5656-5658)aAg>aGg	p.K1886R		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1886					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GCCTTTGCCAAGAGTGGCACC	0.637																																						ENST00000382554.3	1.000000	3.700000e-01	1	5.500000e-01	0.780000	0.772601	0.780000	1.000000																										0				56						c.(5656-5658)aAg>aGg		NYN domain and retroviral integrase containing							12.0	13.0	13.0					14																	24886612		1912	4107	6019	SO:0001583	missense	57523	0	0					g.chr14:24886612A>G	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.5657A>G	chr14.hg19:g.24886612A>G	ENSP00000371994:p.Lys1886Arg	0						p.K1886R	NM_025081.2	NP_079357.2	0	1	1	2.086969	Q9P2P1	NYNRI_HUMAN		9	5975	+			Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	0	1	hg19	c.5657A>G	CCDS45090.1	0	.	.	.	.	.	.	.	.	.	.	A	15.01	2.706588	0.48412	.	.	ENSG00000205978	ENST00000382554	T	0.10960	2.82	4.87	3.72	0.42706	4.87	3.72	0.42706	.	.	.	.	.	T	0.07593	0.0191	N	0.19112	0.55	0.22954	N	0.998512	B	0.15719	0.014	B	0.12156	0.007	T	0.28554	-1.0040	9	0.62326	D	0.03	.	7.2504	0.26146	0.8999:0.0:0.1001:0.0	.	1886	Q9P2P1	NYNRI_HUMAN	R	1886	ENSP00000371994:K1886R	ENSP00000371994:K1886R	K	+	2	0	0	NYNRIN	23956452	23956452	1.000000	0.71417	0.943000	0.38184	0.992000	0.81027	3.953000	0.56699	0.983000	0.38602	0.460000	0.39030	AAG	0.518749		TCGA-2J-AABU-01A-11D-A40W-08	0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1	1	0	1		2	2	2	0		0	0	8		8	8	1	1.830000	-18.771150	1	0.520000				7	7		28	26	1		1	1		0	0	8	0		0.980718	8.798727e-01	0	6	0	12	0	7	28
FBN1	2200	broad.mit.edu	37	15	48714160	48714160	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr15:48714160G>A	ENST00000316623.5	-	61	8014	c.7559C>T	c.(7558-7560)aCg>aTg	p.T2520M		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2520	EGF-like 43; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AATGCAGGACGTATGGTGTTG	0.433																																						ENST00000316623.5	1.000000	6.800000e-01	1	7.800000e-01	0.890000	0.887805	0.890000	1.000000																										0				139	GRCh37	CM074795	FBN1	M		c.(7558-7560)aCg>aTg		fibrillin 1							107.0	92.0	97.0					15																	48714160		2198	4296	6494	SO:0001583	missense	2200	3	121410	34				g.chr15:48714160G>A	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.7559C>T	chr15.hg19:g.48714160G>A	ENSP00000325527:p.Thr2520Met	0						p.T2520M	NM_000138.4	NP_000129	1	2	3	2.101358	P35555	FBN1_HUMAN		61	8014	-		all_lung(180;0.00279)	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	1	1	hg19	c.7559C>T	CCDS32232.1	1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480453	0.63849	.	.	ENSG00000166147	ENST00000316623	D	0.92858	-3.12	6.08	6.08	0.98989	6.08	6.08	0.98989	Growth factor, receptor (1);EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.091594	0.85682	D	0.000000	D	0.95214	0.8448	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.64595	0.927	D	0.93720	0.7032	10	0.40728	T	0.16	.	20.2585	0.98435	0.0:0.0:1.0:0.0	.	2520	P35555	FBN1_HUMAN	M	2520	ENSP00000325527:T2520M	ENSP00000325527:T2520M	T	-	2	0	0	FBN1	46501452	46501452	1.000000	0.71417	0.849000	0.33467	0.618000	0.37518	5.623000	0.67757	2.894000	0.99253	0.655000	0.94253	ACG	0.521245		TCGA-2J-AABU-01A-11D-A40W-08	0.433	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1	1	0	1		2	2	2	0		0	0	54		54	53	1	1.830000	-20.000000	1	0.520000				48	48		159	159	1		1	1		0	0	54	0		1.000000	1	0	6	0	100	0	48	159
FSD2	123722	broad.mit.edu	37	15	83428187	83428187	+	Missense_Mutation	SNP	A	A	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr15:83428187A>T	ENST00000334574.8	-	13	2344	c.2163T>A	c.(2161-2163)ttT>ttA	p.F721L	RP11-752G15.6_ENST00000559366.1_RNA|FSD2_ENST00000541889.1_Missense_Mutation_p.F676L|RP11-752G15.6_ENST00000558174.1_RNA|RP11-752G15.6_ENST00000561107.1_RNA			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	721	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						AGGGATGCACAAATTCGTGAA	0.353																																						ENST00000334574.8	1.000000	6.800000e-01	1	8.200000e-01	0.980000	0.932782	0.980000	1.000000																										0				18						c.(2161-2163)ttT>ttA		fibronectin type III and SPRY domain containing 2							69.0	68.0	68.0					15																	83428187		1850	4099	5949	SO:0001583	missense	123722	0	0					g.chr15:83428187A>T	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.2163T>A	chr15.hg19:g.83428187A>T	ENSP00000335651:p.Phe721Leu	0					FSD2_ENST00000541889.1_Missense_Mutation_p.F676L|RP11-752G15.6_ENST00000559366.1_RNA|RP11-752G15.6_ENST00000561107.1_RNA|RP11-752G15.6_ENST00000558174.1_RNA	p.F721L			0	0	0	2.093065	A1L4K1	FSD2_HUMAN		13	2344	-			B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	1	1	hg19	c.2163T>A	CCDS45332.1	1	.	.	.	.	.	.	.	.	.	.	a	7.160	0.585445	0.13749	.	.	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.12774	2.65;2.65	5.86	0.72	0.18214	5.86	0.72	0.18214	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.615004	0.18017	N	0.154344	T	0.06416	0.0165	N	0.17312	0.475	0.21652	N	0.999601	B;B	0.09022	0.001;0.002	B;B	0.14578	0.008;0.011	T	0.43180	-0.9407	10	0.11485	T	0.65	-4.2398	6.5093	0.22212	0.4824:0.3813:0.1363:0.0	.	676;721	B7ZM02;A1L4K1	.;FSD2_HUMAN	L	721;676	ENSP00000335651:F721L;ENSP00000444078:F676L	ENSP00000335651:F721L	F	-	3	2	2	FSD2	81225241	81225241	0.478000	0.25917	0.213000	0.23690	0.726000	0.41606	-0.045000	0.12003	0.146000	0.19002	-0.319000	0.08680	TTT	0.520000		TCGA-2J-AABU-01A-11D-A40W-08	0.353	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	1	0	1		2	2	2	0		0	0	26		26	26	1	1.830000	-20.000000	1	0.520000	NM_001007122			24	24		69	69	1		1			0	0	26	0		1.000000	0	0	0	0	0	0	24	69
TP53	7157	broad.mit.edu	37	17	7578208	7578208	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr17:7578208T>C	ENST00000269305.4	-	6	830	c.641A>G	c.(640-642)cAt>cGt	p.H214R	TP53_ENST00000359597.4_Missense_Mutation_p.H214R|TP53_ENST00000455263.2_Missense_Mutation_p.H214R|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.H214R|TP53_ENST00000445888.2_Missense_Mutation_p.H214R|TP53_ENST00000420246.2_Missense_Mutation_p.H214R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	214	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> P (in a sporadic cancer; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|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 core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H214R(61)|p.0?(8)|p.?(5)|p.H82R(4)|p.H214fs*33(4)|p.H121R(4)|p.H214fs*5(2)|p.D208fs*1(1)|p.H82fs*>9(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.H121fs*33(1)|p.T211_S215delTFRHS(1)|p.R209fs*6(1)|p.D208_V216delDRNTFRHSV(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CACCACACTATGTCGAAAAGT	0.542		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	ENST00000269305.4	1.000000	8.300000e-01	1	9.100000e-01	0.960000	0.958405	0.960000	1.000000		111	yes	Rec	yes	Li-Fraumeni syndrome	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	17p13	7157	Mis, N, F	tumor protein p53				"""L, E, M, O"""	L, E, M, O		breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types	breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types		98	Substitution - Missense(69)|Deletion - Frameshift(12)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(3)|Complex - deletion inframe(1)	p.H214R(61)|p.0?(8)|p.?(5)|p.H82R(4)|p.H214fs*33(4)|p.H121R(4)|p.H214fs*5(2)|p.D208fs*1(1)|p.H82fs*>9(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213fs*32(1)|p.H121fs*33(1)|p.T211_S215delTFRHS(1)|p.R209fs*6(1)|p.D208_V216delDRNTFRHSV(1)	lung(27)|liver(12)|ovary(8)|biliary_tract(6)|oesophagus(6)|upper_aerodigestive_tract(5)|central_nervous_system(5)|large_intestine(5)|urinary_tract(5)|prostate(4)|bone(4)|stomach(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|soft_tissue(1)|skin(1)|pancreas(1)	24185						c.(640-642)cAt>cGt	Other conserved DNA damage response genes	tumor protein p53	Acetylsalicylic acid(DB00945)						127.0	114.0	119.0					17																	7578208		2203	4300	6503	SO:0001583	missense	7157	0	0		Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	g.chr17:7578208T>C	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.641A>G	chr17.hg19:g.7578208T>C	ENSP00000269305:p.His214Arg	1	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_ENST00000445888.2_Missense_Mutation_p.H214R|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.H214R|TP53_ENST00000420246.2_Missense_Mutation_p.H214R|TP53_ENST00000359597.4_Missense_Mutation_p.H214R|TP53_ENST00000413465.2_Missense_Mutation_p.H214R	p.H214R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	0	1	1	1.589102	P04637	P53_HUMAN		6	830	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	1	1	hg19	c.641A>G	CCDS11118.1	1	.	.	.	.	.	.	.	.	.	.	T	35	5.548167	0.96488	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99755	-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64;-6.64	5.28	5.28	0.74379	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.052737	0.85682	D	0.000000	D	0.99664	0.9875	M	0.75615	2.305	0.80722	D	1	D;D;P;D;D;D;D	0.76494	0.999;0.992;0.733;0.999;0.994;0.994;0.999	D;D;B;D;D;D;D	0.74674	0.984;0.947;0.376;0.982;0.95;0.968;0.962	D	0.97475	1.0043	10	0.72032	D	0.01	-26.1151	13.4753	0.61306	0.0:0.0:0.0:1.0	.	175;214;214;121;214;214;214	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	214;214;214;214;214;214;203;121;82;121;82	ENSP00000410739:H214R;ENSP00000352610:H214R;ENSP00000269305:H214R;ENSP00000398846:H214R;ENSP00000391127:H214R;ENSP00000391478:H214R;ENSP00000425104:H82R;ENSP00000423862:H121R	ENSP00000269305:H214R	H	-	2	0	0	TP53	7518933	7518933	1.000000	0.71417	0.283000	0.24790	0.961000	0.63080	7.996000	0.88334	2.128000	0.65567	0.460000	0.39030	CAT	0.353622		TCGA-2J-AABU-01A-11D-A40W-08	0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1		2	2	2	0		0	0	41		41	41	1	1.830000	-20.000000	1	0.520000	NM_000546			52	52		73	72	1		1	1	1	0	0	41	920		1.000000	9.879510e-01	1	6	234	7	478	52	73
ADAM11	4185	broad.mit.edu	37	17	42851860	42851860	+	Splice_Site	SNP	T	T	C			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr17:42851860T>C	ENST00000200557.6	+	13	1247	c.1078T>C	c.(1078-1080)Tac>Cac	p.Y360H	ADAM11_ENST00000535346.1_Splice_Site_p.Y160H	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	360	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				CCACCCCCAGTACGGCAACAT	0.632																																						ENST00000200557.6	1.000000	6.300000e-01	1	7.600000e-01	0.920000	0.895788	0.920000	1.000000																										0				33						c.(1078-1080)Tac>Cac		ADAM metallopeptidase domain 11							40.0	37.0	38.0					17																	42851860		2202	4300	6502	SO:0001630	splice_region_variant	4185	0	0					g.chr17:42851860T>C	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"""ADAM metallopeptidase domain containing"""	189	protein-coding gene	gene with protein product	"""metalloproteinase-like, disintegrin-like, cysteine-rich protein"""	155120	"""a disintegrin and metalloproteinase domain 11"""	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.1078-1T>C	chr17.hg19:g.42851860T>C		0					ADAM11_ENST00000535346.1_Splice_Site_p.Y160H	p.Y360H	NM_002390.4	NP_002381.2	1	2	3	2.137818	O75078	ADA11_HUMAN		13	1247	+		Prostate(33;0.0959)	Q14808|Q14809|Q14810	Splice_Site	SNP	ENST00000200557.6	1	0	hg19	c.1078T>C	CCDS11486.1	1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.812808	0.90707	.	.	ENSG00000073670	ENST00000200557;ENST00000535346;ENST00000355638	T;T	0.09817	2.94;2.94	5.04	5.04	0.67666	5.04	5.04	0.67666	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.213347	0.41605	D	0.000843	T	0.23926	0.0579	L	0.45051	1.395	0.80722	D	1	D;D	0.76494	0.993;0.999	D;D	0.73708	0.98;0.981	T	0.00675	-1.1615	9	.	.	.	.	13.8849	0.63702	0.0:0.0:0.0:1.0	.	160;360	B4DKD2;O75078	.;ADA11_HUMAN	H	360;160;260	ENSP00000200557:Y360H;ENSP00000443773:Y160H	.	Y	+	1	0	0	ADAM11	40207386	40207386	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.862000	0.69560	2.111000	0.64477	0.379000	0.24179	TAC	0.526160		TCGA-2J-AABU-01A-11D-A40W-08	0.632	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	1	0	1		2	2	2	0		0	0	34		34	33	1	1.830000	-20.000000	1	0.520000	NM_002390	Missense_Mutation		26	25		85	85	1		1			0	0	34	0		1.000000	0	0	0	0	0	0	26	85
ATP8B3	148229	broad.mit.edu	37	19	1785511	1785511	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr19:1785511G>A	ENST00000310127.6	-	26	3588	c.3350C>T	c.(3349-3351)gCg>gTg	p.A1117V	ATP8B3_ENST00000539485.1_Missense_Mutation_p.A1127V|ATP8B3_ENST00000525591.1_Missense_Mutation_p.A1080V	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1117					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCACGACCGCAAAGGACTG	0.637																																						ENST00000310127.6	0.190000	2.000000e-02	1.400000e-01	5.000000e-02	0.080000	0.096579	0.080000	0.080000																										0				23						c.(3349-3351)gCg>gTg		ATPase, aminophospholipid transporter, class I, type 8B, member 3							37.0	45.0	42.0					19																	1785511		2064	4182	6246	SO:0001583	missense	148229	5	120970	35				g.chr19:1785511G>A	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3350C>T	chr19.hg19:g.1785511G>A	ENSP00000311336:p.Ala1117Val	1					ATP8B3_ENST00000539485.1_Missense_Mutation_p.A1127V|ATP8B3_ENST00000525591.1_Missense_Mutation_p.A1080V	p.A1117V	NM_138813.3	NP_620168.1	0	1	1	1.614889	O60423	AT8B3_HUMAN		26	3588	-		Hepatocellular(1079;0.137)	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	0	1	hg19	c.3350C>T	CCDS45901.1	0	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777695	0.70107	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.41400	1.0;1.0;1.0	4.48	0.765	0.18470	4.48	0.765	0.18470	.	0.470389	0.21414	N	0.074937	T	0.52964	0.1767	M	0.72118	2.19	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.53760	0.51;0.734	T	0.55042	-0.8202	10	0.87932	D	0	.	14.0541	0.64756	0.0:0.4546:0.5454:0.0	.	1117;1080	O60423;Q7Z485	AT8B3_HUMAN;.	V	1117;1127;1080	ENSP00000311336:A1117V;ENSP00000443574:A1127V;ENSP00000437115:A1080V	ENSP00000311336:A1117V	A	-	2	0	0	ATP8B3	1736511	1736511	0.992000	0.36948	0.000000	0.03702	0.063000	0.16089	6.399000	0.73248	-0.033000	0.13736	-0.175000	0.13238	GCG	0.353622		TCGA-2J-AABU-01A-11D-A40W-08	0.637	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	0	0	1		2	2	2	0		0	0	53		53	50	1	1.830000	-3.326518	1	0.520000	NM_138813			4	4		140	126	0		1			0	0	53	0		0.865657	0	0	0	0	0	0	4	140
C19orf35	374872	broad.mit.edu	37	19	2278825	2278825	+	Missense_Mutation	SNP	A	A	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr19:2278825A>T	ENST00000342063.3	-	3	463	c.370T>A	c.(370-372)Tcc>Acc	p.S124T		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	124										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGCGGAGGGAGAGGCCCAGT	0.687																																						ENST00000342063.3	0.860000	2.200000e-01	6.900000e-01	3.400000e-01	0.500000	0.522572	0.500000	0.480000																										0				8						c.(370-372)Tcc>Acc		chromosome 19 open reading frame 35							9.0	10.0	10.0					19																	2278825		2181	4282	6463	SO:0001583	missense	374872	0	0					g.chr19:2278825A>T	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.370T>A	chr19.hg19:g.2278825A>T	ENSP00000345102:p.Ser124Thr	1						p.S124T	NM_198532.2	NP_940934.1	0	1	1	1.614889	Q6ZS72	CS035_HUMAN		3	463	-				Missense_Mutation	SNP	ENST00000342063.3	0	1	hg19	c.370T>A	CCDS12087.1	0	.	.	.	.	.	.	.	.	.	.	A	7.514	0.655242	0.14580	.	.	ENSG00000188305	ENST00000342063	T	0.14144	2.53	4.16	-0.449	0.12226	4.16	-0.449	0.12226	.	.	.	.	.	T	0.08179	0.0204	L	0.47716	1.5	0.09310	N	1	P	0.35982	0.531	B	0.29176	0.099	T	0.37103	-0.9720	9	0.11485	T	0.65	.	4.3547	0.11172	0.4382:0.0:0.3987:0.1632	.	124	Q6ZS72	CS035_HUMAN	T	124	ENSP00000345102:S124T	ENSP00000345102:S124T	S	-	1	0	0	C19orf35	2229825	2229825	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.277000	0.08502	-0.538000	0.06281	0.363000	0.22086	TCC	0.353622		TCGA-2J-AABU-01A-11D-A40W-08	0.687	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	0	0	1		2	2	2	0		0	0	13		13	12	1	1.830000	-13.880320	1	0.520000	NM_198532			6	6		28	28	1		1			0	0	13	0		0.969841	0	0	0	0	0	0	6	28
PSG3	5671	broad.mit.edu	37	19	43237088	43237088	+	Missense_Mutation	SNP	C	C	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr19:43237088C>T	ENST00000327495.5	-	3	741	c.557G>A	c.(556-558)aGc>aAc	p.S186N	PSG3_ENST00000595140.1_Missense_Mutation_p.S186N|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	186	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CATAGGGAGGCTCTGACCATT	0.488																																						ENST00000327495.5			0	0																														0				36						c.(556-558)aGc>aAc		pregnancy specific beta-1-glycoprotein 3							231.0	230.0	230.0					19																	43237088		2203	4300	6503	SO:0001583	missense	5671	0	0					g.chr19:43237088C>T		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.557G>A	chr19.hg19:g.43237088C>T	ENSP00000332215:p.Ser186Asn						PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Missense_Mutation_p.S186N	p.S186N	NM_021016.3	NP_066296.2					Q16557	PSG3_HUMAN		3	741	-		Prostate(69;0.00682)	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	1	1	hg19	c.557G>A	CCDS12611.1		.	.	.	.	.	.	.	.	.	.	-	7.246	0.602252	0.13939	.	.	ENSG00000221826	ENST00000327495	T	0.12361	2.69	1.59	-1.53	0.08611	1.59	-1.53	0.08611	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.12774	0.0310	M	0.64567	1.98	0.09310	N	1	B;B	0.28378	0.209;0.006	B;B	0.30782	0.12;0.012	T	0.36212	-0.9757	9	0.54805	T	0.06	.	2.5923	0.04846	0.0:0.4556:0.3146:0.2298	.	164;186	Q08266;Q16557	.;PSG3_HUMAN	N	186	ENSP00000332215:S186N	ENSP00000332215:S186N	S	-	2	0	0	PSG3	47928928	47928928	0.000000	0.05858	0.015000	0.15790	0.038000	0.13279	-0.592000	0.05747	0.021000	0.15133	0.393000	0.25936	AGC			TCGA-2J-AABU-01A-11D-A40W-08	0.488	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	1	0	1		2	2	2	0		0	0	309		309	316	1	1.830000	-20.000000	1	0.520000	NM_021016			247	241		852	828	1		1			0	0	309	0		1.000000	0	0	0	0	0	0	247	852
PNKP	11284	broad.mit.edu	37	19	50365046	50365046	+	Silent	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr19:50365046G>A	ENST00000322344.3	-	14	1390	c.1281C>T	c.(1279-1281)gaC>gaT	p.D427D	AC018766.5_ENST00000601893.1_RNA|PNKP_ENST00000596014.1_Silent_p.D427D|AC018766.4_ENST00000596624.1_RNA|AC018766.5_ENST00000593654.1_RNA|PNKP_ENST00000600573.1_Silent_p.D396D|PNKP_ENST00000600910.1_Intron|AC018766.5_ENST00000599259.1_RNA	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	427	Kinase. {ECO:0000250}.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GGCTCGCGGCGTCTGGGTTTG	0.687								Other BER factors																														ENST00000322344.3	1.000000	4.100000e-01	1	5.900000e-01	0.820000	0.803806	0.820000	1.000000																										0				19						c.(1279-1281)gaC>gaT	Other BER factors	polynucleotide kinase 3'-phosphatase																																				SO:0001819	synonymous_variant	11284	10	118868	37				g.chr19:50365046G>A	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.1281C>T	chr19.hg19:g.50365046G>A		1					PNKP_ENST00000600910.1_Intron|PNKP_ENST00000600573.1_Silent_p.D396D|AC018766.5_ENST00000599259.1_RNA|PNKP_ENST00000596014.1_Silent_p.D427D|AC018766.5_ENST00000593654.1_RNA|AC018766.5_ENST00000601893.1_RNA|AC018766.4_ENST00000596624.1_RNA	p.D427D	NM_007254.3	NP_009185.2	0	1	1	1.746683	Q96T60	PNKP_HUMAN		14	1390	-		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Silent	SNP	ENST00000322344.3	0	1	hg19	c.1281C>T	CCDS12783.1	0																																																																																								0.403727		TCGA-2J-AABU-01A-11D-A40W-08	0.687	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	1	0	1		2	2	2	0		0	0	10		10	10	1	1.830000	-17.026380	1	0.520000	NM_007254			7	6		18	15	0		1	1		0	0	10	0		0.973630	9.629777e-01	0	6	0	13	0	7	18
ZNF160	90338	broad.mit.edu	37	19	53572263	53572263	+	Silent	SNP	A	A	C			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr19:53572263A>C	ENST00000429604.1	-	7	1939	c.1524T>G	c.(1522-1524)ccT>ccG	p.P508P	ZNF160_ENST00000599056.1_Silent_p.P508P|ZNF160_ENST00000418871.1_Silent_p.P508P|ZNF160_ENST00000601421.1_Silent_p.P472P	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	508					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TACACTTGTAAGGTTTCTCTC	0.383																																						ENST00000429604.1	1.000000	8.100000e-01	1	8.900000e-01	0.970000	0.957726	0.970000	1.000000																										0				35						c.(1522-1524)ccT>ccG		zinc finger protein 160							100.0	101.0	101.0					19																	53572263		2203	4300	6503	SO:0001819	synonymous_variant	90338	0	0					g.chr19:53572263A>C	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1524T>G	chr19.hg19:g.53572263A>C		0					ZNF160_ENST00000599056.1_Silent_p.P508P|ZNF160_ENST00000601421.1_Silent_p.P472P|ZNF160_ENST00000418871.1_Silent_p.P508P	p.P508P	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	1	2	3	2.140422	Q9HCG1	ZN160_HUMAN		7	1939	-			Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	1	1	hg19	c.1524T>G	CCDS12859.1	1																																																																																								0.526160		TCGA-2J-AABU-01A-11D-A40W-08	0.383	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	1	0	1		2	2	2	0		0	0	155		155	155	1	1.830000	-20.000000	1	0.520000	NM_033288			100	100		298	291	1		1	1		0	0	155	0		1.000000	1.597685e-01	0	3	0	0	0	100	298
COL24A1	255631	broad.mit.edu	37	1	86196283	86196283	+	Silent	SNP	A	A	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr1:86196283A>G	ENST00000370571.2	-	60	5457	c.5091T>C	c.(5089-5091)caT>caC	p.H1697H	COL24A1_ENST00000436319.1_Silent_p.H1676H	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1697	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CAGTTTTGAGATGAGGAAGTT	0.393																																						ENST00000370571.2	1.000000	8.400000e-01	1	9.400000e-01	0.990000	0.981005	0.990000	1.000000																										0				101						c.(5089-5091)caT>caC		collagen, type XXIV, alpha 1							144.0	135.0	138.0					1																	86196283		1869	4101	5970	SO:0001819	synonymous_variant	255631	0	0					g.chr1:86196283A>G	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.5091T>C	chr1.hg19:g.86196283A>G		0					COL24A1_ENST00000436319.1_Silent_p.H1676H	p.H1697H	NM_152890.5	NP_690850.2	1	2	3	2.142653	Q17RW2	COOA1_HUMAN		60	5457	-			C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	1	1	hg19	c.5091T>C	CCDS41353.1	1																																																																																								0.526160		TCGA-2J-AABU-01A-11D-A40W-08	0.393	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	1	0	1		2	2	2	0		0	0	75		75	73	1	1.830000	-20.000000	1	0.520000	NM_152890			68	67		183	181	1		1	0		0	0	75	0		1.000000	3.012061e-01	0	0	0	4	0	68	183
SLC5A3	6526	broad.mit.edu	37	21	35468701	35468701	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr21:35468701G>A	ENST00000381151.3	+	2	1716	c.1204G>A	c.(1204-1206)Gca>Aca	p.A402T	AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.A402T|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	402					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						CCGCAAGAGCGCAAGCTCCCG	0.478																																						ENST00000381151.3	0.140000	2.000000e-02	1.100000e-01	4.000000e-02	0.060000	0.078015	0.060000	0.070000																										0				20						c.(1204-1206)Gca>Aca		solute carrier family 5 (sodium/myo-inositol cotransporter), member 3							89.0	81.0	84.0					21																	35468701		2203	4300	6503	SO:0001583	missense	6526	0	0					g.chr21:35468701G>A		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"""Solute carriers"""	11038	protein-coding gene	gene with protein product		600444	"""solute carrier family 5 (inositol transporter), member 3"""			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1204G>A	chr21.hg19:g.35468701G>A	ENSP00000370543:p.Ala402Thr	1					MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.A402T	p.A402T			0	1	1	1.570314	P53794	SC5A3_HUMAN		2	1716	+			O43489	Missense_Mutation	SNP	ENST00000381151.3	0	1	hg19	c.1204G>A	CCDS33549.1	0	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122917	0.77436	.	.	ENSG00000198743	ENST00000381151	D	0.89196	-2.48	5.69	5.69	0.88448	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.94301	0.8169	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.94516	0.7723	10	0.87932	D	0	.	18.5913	0.91214	0.0:0.0:1.0:0.0	.	402	P53794	SC5A3_HUMAN	T	402	ENSP00000370543:A402T	ENSP00000370543:A402T	A	+	1	0	0	SLC5A3	34390571	34390571	1.000000	0.71417	0.584000	0.28653	0.979000	0.70002	7.792000	0.85828	2.677000	0.91161	0.655000	0.94253	GCA	0.351351		TCGA-2J-AABU-01A-11D-A40W-08	0.478	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1	0	0	1		2	2	2	0		0	0	83		83	83	1	1.830000	-2.768101	1	0.520000				5	5		210	209	0		1			0	0	83	0		0.937507	0	0	0	0	0	0	5	210
THSD7B	80731	broad.mit.edu	37	2	138163324	138163324	+	Missense_Mutation	SNP	C	C	T	rs200743398	byFrequency	TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr2:138163324C>T	ENST00000409968.1	+	13	2820	c.2642C>T	c.(2641-2643)aCg>aTg	p.T881M	THSD7B_ENST00000413152.2_Missense_Mutation_p.T850M|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Missense_Mutation_p.T881M			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	881	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TCCAAGTTTACGCCCTGCTCC	0.502													C|||	2	0.000399361	0.0	0.0029	5008	,	,		17720	0.0		0.0	False		,,,				2504	0.0					ENST00000409968.1	1.000000	6.400000e-01	1	7.800000e-01	0.930000	0.905894	0.930000	1.000000																										0				134						c.(2641-2643)aCg>aTg		thrombospondin, type I, domain containing 7B		C	MET/THR	0,4074		0,0,2037	71.0	74.0	73.0		2549	5.6	1.0	2		73	3,8349		0,3,4173	yes	missense	THSD7B	NM_001080427.1	81	0,3,6210	TT,TC,CC		0.0359,0.0,0.0241	probably-damaging	850/1578	138163324	3,12423	2037	4176	6213	SO:0001583	missense	80731	12	120882	39				g.chr2:138163324C>T			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2642C>T	chr2.hg19:g.138163324C>T	ENSP00000387145:p.Thr881Met	0					THSD7B_ENST00000272643.3_Missense_Mutation_p.T881M|THSD7B_ENST00000413152.2_Missense_Mutation_p.T850M|THSD7B_ENST00000543459.1_Intron	p.T881M			0	0	0	2.074030	Q9C0I4	THS7B_HUMAN		13	2820	+				Missense_Mutation	SNP	ENST00000409968.1	1	1	hg19	c.2642C>T		1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393937	0.62066	0.0	3.59E-4	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.62232	0.04;0.04;0.04	5.59	5.59	0.84812	5.59	5.59	0.84812	.	0.105674	0.64402	D	0.000003	T	0.77003	0.4067	L	0.55481	1.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.77710	-0.2486	10	0.66056	D	0.02	.	19.5832	0.95478	0.0:1.0:0.0:0.0	.	881;850	Q9C0I4;C9JKN6	THS7B_HUMAN;.	M	881;881;850	ENSP00000387145:T881M;ENSP00000272643:T881M;ENSP00000413841:T850M	ENSP00000272643:T881M	T	+	2	0	0	THSD7B	137879794	137879794	0.999000	0.42202	0.966000	0.40874	0.381000	0.30169	4.450000	0.60041	2.633000	0.89246	0.591000	0.81541	ACG	0.517491		TCGA-2J-AABU-01A-11D-A40W-08	0.502	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	0	0	1		2	2	2	0		0	0	27		27	26	1	1.830000	-20.000000	1	0.520000	XM_046570.9			25	25		77	76	1		1			0	0	27	0		1.000000	0	0	0	0	0	0	25	77
NRXN1	9378	broad.mit.edu	37	2	50765572	50765572	+	Missense_Mutation	SNP	T	T	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr2:50765572T>G	ENST00000406316.2	-	10	3438	c.1962A>C	c.(1960-1962)aaA>aaC	p.K654N	NRXN1_ENST00000402717.3_Missense_Mutation_p.K646N|NRXN1_ENST00000404971.1_Missense_Mutation_p.K694N|NRXN1_ENST00000401669.2_Missense_Mutation_p.K654N|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000406859.3_Missense_Mutation_p.K654N|NRXN1_ENST00000405472.3_Missense_Mutation_p.K646N	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	654	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCCGGATATCTTTGCTTTGGC	0.498																																						ENST00000406316.2	1.000000	9.400000e-01	1	9.900000e-01	0.990000	0.996294	0.990000	1.000000																										0				58						c.(1960-1962)aaA>aaC		neurexin 1							249.0	261.0	257.0					2																	50765572		2195	4297	6492	SO:0001583	missense	9378	0	0					g.chr2:50765572T>G	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1962A>C	chr2.hg19:g.50765572T>G	ENSP00000384311:p.Lys654Asn	1					NRXN1_ENST00000406859.3_Missense_Mutation_p.K654N|NRXN1_ENST00000404971.1_Missense_Mutation_p.K694N|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Missense_Mutation_p.K654N|NRXN1_ENST00000402717.3_Missense_Mutation_p.K646N|NRXN1_ENST00000405472.3_Missense_Mutation_p.K646N	p.K654N	NM_004801.4	NP_004792.1	1	2	3	2.642762	Q9ULB1	NRX1A_HUMAN	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)	10	3438	-		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	1	1	hg19	c.1962A>C	CCDS54360.1	1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.381063	0.61845	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.16	4.01	0.46588	5.16	4.01	0.46588	.	0.000000	0.85682	D	0.000000	D	0.83982	0.5372	M	0.66939	2.045	0.36502	D	0.869045	D;D;P	0.61697	0.99;0.967;0.729	P;P;B	0.62885	0.908;0.592;0.334	D	0.87073	0.2161	10	0.66056	D	0.02	.	10.8231	0.46617	0.0:0.074:0.0:0.926	.	694;654;646	Q9ULB1-3;F8WB18;A7E294	.;.;.	N	694;654;646;654;695;646;654	ENSP00000385142:K694N;ENSP00000384311:K654N;ENSP00000434015:K646N;ENSP00000385017:K654N;ENSP00000385434:K646N;ENSP00000385681:K654N	ENSP00000385017:K654N	K	-	3	2	2	NRXN1	50619076	50619076	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.923000	0.28757	0.983000	0.38602	0.477000	0.44152	AAA	0.619048		TCGA-2J-AABU-01A-11D-A40W-08	0.498	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2	1	0	1		2	2	2	0		0	0	330		330	326	1	1.830000	-20.000000	1	0.520000				292	292		1043	1034	1		1			0	0	330	0		1.000000	0	0	0	0	0	0	292	1043
KIAA1841	84542	broad.mit.edu	37	2	61304193	61304193	+	Silent	SNP	G	G	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr2:61304193G>T	ENST00000402291.1	+	6	811	c.570G>T	c.(568-570)gtG>gtT	p.V190V	KIAA1841_ENST00000453873.1_Silent_p.V190V|KIAA1841_ENST00000295031.5_Silent_p.V190V|KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000356719.2_Silent_p.V190V	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	190										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			GGGAAGAGGTGGACATTTCAG	0.378																																						ENST00000402291.1	0.240000	9.000000e-02	2.100000e-01	1.200000e-01	0.160000	0.170628	0.160000	0.160000																										0				25						c.(568-570)gtG>gtT		KIAA1841							106.0	109.0	108.0					2																	61304193		2203	4300	6503	SO:0001819	synonymous_variant	84542	0	0					g.chr2:61304193G>T	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.570G>T	chr2.hg19:g.61304193G>T		1					KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000356719.2_Silent_p.V190V|KIAA1841_ENST00000295031.5_Silent_p.V190V|KIAA1841_ENST00000453873.1_Silent_p.V190V	p.V190V	NM_001129993.1	NP_001123465.1	1	2	3	2.642762	Q6NSI8	K1841_HUMAN	Epithelial(17;0.193)	6	811	+			Q49AF0|Q6ZND0|Q96JI6	Silent	SNP	ENST00000402291.1	1	1	hg19	c.570G>T	CCDS46296.1	0																																																																																								0.619048		TCGA-2J-AABU-01A-11D-A40W-08	0.378	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	1	0	1		2	2	2	0		0	0	144		144	144	1	1.830000	-2.989408	1	0.520000	NM_032506			23	23		656	644	0		1	0		0	0	144	0		0.999999	3.755475e-03	0	0	0	3	0	23	656
LRRTM4	80059	broad.mit.edu	37	2	77745555	77745555	+	Silent	SNP	A	A	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr2:77745555A>G	ENST00000409093.1	-	3	1776	c.1440T>C	c.(1438-1440)ccT>ccC	p.P480P	LRRTM4_ENST00000409282.1_Silent_p.P481P|LRRTM4_ENST00000409088.3_Silent_p.P480P|LRRTM4_ENST00000409911.1_Silent_p.P481P|LRRTM4_ENST00000409884.1_Silent_p.P480P			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	480					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		ACTCCTGTAAAGGGGAATTCA	0.473																																						ENST00000409093.1	1.000000	5.600000e-01	9.500000e-01	6.700000e-01	0.810000	0.814960	0.810000	1.000000																										0				64						c.(1438-1440)ccT>ccC		leucine rich repeat transmembrane neuronal 4							91.0	88.0	89.0					2																	77745555		1871	4108	5979	SO:0001819	synonymous_variant	80059	0	0					g.chr2:77745555A>G	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.1440T>C	chr2.hg19:g.77745555A>G		0					LRRTM4_ENST00000409911.1_Silent_p.P481P|LRRTM4_ENST00000409282.1_Silent_p.P481P|LRRTM4_ENST00000409884.1_Silent_p.P480P|LRRTM4_ENST00000409088.3_Silent_p.P480P	p.P480P			0	0	0	2.095781	Q86VH4	LRRT4_HUMAN		3	1776	-			Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	1	1	hg19	c.1440T>C	CCDS46346.1	0																																																																																								0.520000		TCGA-2J-AABU-01A-11D-A40W-08	0.473	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	1	0	0		2	2	2	0		0	0	39		39	39	1	1.830000	-18.740340	1	0.520000	NM_024993			27	27		101	101	1		1			0	0	39	0		1.000000	0	0	0	0	0	0	27	101
KIF5C	3800	broad.mit.edu	37	2	149854968	149854968	+	Missense_Mutation	SNP	T	T	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr2:149854968T>A	ENST00000435030.1	+	19	2523	c.2155T>A	c.(2155-2157)Tcc>Acc	p.S719T	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Missense_Mutation_p.S624T|KIF5C_ENST00000397413.1_Missense_Mutation_p.S487T			O60282	KIF5C_HUMAN	kinesin family member 5C	719					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GAAGCAGCTGTCCAGACTCCG	0.572																																						ENST00000435030.1	1.000000	3.000000e-01	1	4.800000e-01	0.730000	0.730651	0.730000	1.000000																										0				36						c.(2155-2157)Tcc>Acc		kinesin family member 5C							22.0	26.0	25.0					2																	149854968		2073	4224	6297	SO:0001583	missense	3800	0	0					g.chr2:149854968T>A	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2155T>A	chr2.hg19:g.149854968T>A	ENSP00000393379:p.Ser719Thr	0					KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Missense_Mutation_p.S487T|KIF5C_ENST00000414838.2_Missense_Mutation_p.S624T	p.S719T			0	0	0	2.074030	O60282	KIF5C_HUMAN		19	2523	+			O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	0	1	hg19	c.2155T>A		0	.	.	.	.	.	.	.	.	.	.	T	25.9	4.685940	0.88639	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	T;T;T	0.79845	-1.31;-1.31;-1.31	5.78	5.78	0.91487	5.78	5.78	0.91487	.	0.126390	0.56097	D	0.000025	T	0.76147	0.3947	.	.	.	0.44918	D	0.997937	P	0.37233	0.588	B	0.38264	0.269	T	0.74478	-0.3652	8	.	.	.	.	16.1254	0.81392	0.0:0.0:0.0:1.0	.	719	O60282	KIF5C_HUMAN	T	719;624;622;487	ENSP00000393379:S719T;ENSP00000410115:S624T;ENSP00000380560:S487T	.	S	+	1	0	0	KIF5C	149563214	149563214	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.204000	0.65180	2.195000	0.70347	0.528000	0.53228	TCC	0.517491		TCGA-2J-AABU-01A-11D-A40W-08	0.572	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	0	0	1		2	2	2	0		0	0	8		8	8	1	1.830000	-12.143630	1	0.520000	NM_004522			5	5		22	21	0		1	0		0	0	8	0		0.938005	4.827586e-02	0	0	0	2	0	5	22
SLIT2	9353	broad.mit.edu	37	4	20618553	20618553	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr4:20618553G>A	ENST00000504154.1	+	35	4120	c.3868G>A	c.(3868-3870)Gtg>Atg	p.V1290M	SLIT2_ENST00000503837.1_Missense_Mutation_p.V1286M|SLIT2_ENST00000273739.5_Missense_Mutation_p.V1303M|SLIT2_ENST00000503823.1_Missense_Mutation_p.V1282M	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1290	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GAAGAGTAACGTGGCATCTCT	0.562																																						ENST00000504154.1	1.000000	7.300000e-01	1	8.300000e-01	0.930000	0.924107	0.930000	1.000000																										0				116						c.(3868-3870)Gtg>Atg		slit homolog 2 (Drosophila)							44.0	43.0	43.0					4																	20618553		2203	4300	6503	SO:0001583	missense	9353	14	121408	39				g.chr4:20618553G>A	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.3868G>A	chr4.hg19:g.20618553G>A	ENSP00000422591:p.Val1290Met	0					SLIT2_ENST00000273739.5_Missense_Mutation_p.V1303M|SLIT2_ENST00000503837.1_Missense_Mutation_p.V1286M|SLIT2_ENST00000503823.1_Missense_Mutation_p.V1282M	p.V1290M	NM_004787.1	NP_004778.1	1	2	3	2.117417	O94813	SLIT2_HUMAN		35	4120	+			B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	1	1	hg19	c.3868G>A	CCDS3426.1	1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.062304	0.55432	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.96	5.11	0.69529	5.96	5.11	0.69529	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.919326	0.09535	N	0.788994	T	0.60702	0.2289	N	0.25890	0.77	0.28499	N	0.914096	P;P	0.41673	0.759;0.678	B;B	0.35413	0.197;0.202	T	0.55418	-0.8144	10	0.45353	T	0.12	.	10.0633	0.42288	0.2:0.0:0.8:0.0	.	1282;1290	O94813-3;O94813	.;SLIT2_HUMAN	M	1282;1290;1303;1286;1286	ENSP00000427548:V1282M;ENSP00000422591:V1290M;ENSP00000273739:V1303M;ENSP00000422261:V1286M	ENSP00000273739:V1303M	V	+	1	0	0	SLIT2	20227651	20227651	0.979000	0.34478	0.997000	0.53966	0.989000	0.77384	1.895000	0.39778	2.833000	0.97629	0.650000	0.86243	GTG	0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.562	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2	1	0	1		2	2	2	0		0	0	41		41	40	1	1.830000	-20.000000	1	0.520000				55	55		171	167	1		1	0		0	0	41	0		1.000000	6.113537e-02	0	0	0	2	0	55	171
TLR6	10333	broad.mit.edu	37	4	38830535	38830535	+	Missense_Mutation	SNP	T	T	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr4:38830535T>A	ENST00000381950.1	-	1	625	c.560A>T	c.(559-561)gAg>gTg	p.E187V	TLR6_ENST00000436693.2_Missense_Mutation_p.E187V			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	187					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTTTCTGTCTCATTTTCTTT	0.318																																						ENST00000381950.1	0.240000	2.000000e-02	1.600000e-01	5.000000e-02	0.100000	0.120477	0.100000	0.090000																										0				22						c.(559-561)gAg>gTg		toll-like receptor 6							30.0	33.0	32.0					4																	38830535		2193	4299	6492	SO:0001583	missense	10333	0	0					g.chr4:38830535T>A		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.560A>T	chr4.hg19:g.38830535T>A	ENSP00000371376:p.Glu187Val	0					TLR6_ENST00000436693.2_Missense_Mutation_p.E187V	p.E187V			1	2	3	2.117417	Q9Y2C9	TLR6_HUMAN		1	625	-			B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	0	1	hg19	c.560A>T	CCDS3446.1	0	.	.	.	.	.	.	.	.	.	.	T	6.087	0.384310	0.11524	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.02301	4.35;4.35	5.44	1.66	0.24008	5.44	1.66	0.24008	.	0.426300	0.23090	N	0.052057	T	0.03564	0.0102	M	0.77103	2.36	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.33523	-0.9865	10	0.87932	D	0	.	4.5985	0.12341	0.1363:0.2183:0.0:0.6454	.	187	Q9Y2C9	TLR6_HUMAN	V	187	ENSP00000389600:E187V;ENSP00000371376:E187V	ENSP00000371376:E187V	E	-	2	0	0	TLR6	38506930	38506930	0.005000	0.15991	0.001000	0.08648	0.507000	0.33981	0.664000	0.25068	0.350000	0.24002	0.260000	0.18958	GAG	0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.318	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1	0	0	1		2	2	2	0		0	0	36		36	36	1	1.830000	-3.454353	1	0.520000				4	4		166	166	0		1			0	0	36	0		0.891327	0	0	0	0	0	0	4	166
ARHGAP24	83478	broad.mit.edu	37	4	86898803	86898803	+	Missense_Mutation	SNP	T	T	C			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr4:86898803T>C	ENST00000395184.1	+	8	1353	c.887T>C	c.(886-888)aTc>aCc	p.I296T	ARHGAP24_ENST00000395183.2_Missense_Mutation_p.I201T|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.I203T	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	296	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GGTCCTAATATCCTGCGCCCC	0.398																																						ENST00000395184.1	1.000000	6.300000e-01	9.200000e-01	7.200000e-01	0.810000	0.821867	0.810000	0.820000																										0				24						c.(886-888)aTc>aCc		Rho GTPase activating protein 24							126.0	111.0	116.0					4																	86898803		2203	4300	6503	SO:0001583	missense	83478	0	0					g.chr4:86898803T>C	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.887T>C	chr4.hg19:g.86898803T>C	ENSP00000378611:p.Ile296Thr	0					ARHGAP24_ENST00000395183.2_Missense_Mutation_p.I201T|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.I203T	p.I296T	NM_001025616.2	NP_001020787.2	1	2	3	2.117417	Q8N264	RHG24_HUMAN		8	1353	+		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	1	1	hg19	c.887T>C	CCDS34025.1	0	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852845	0.91355	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.95	5.95	0.96441	5.95	5.95	0.96441	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.78679	0.4321	H	0.95402	3.665	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.996;0.986;0.999	D	0.85343	0.1097	10	0.87932	D	0	.	16.4069	0.83677	0.0:0.0:0.0:1.0	.	201;203;296	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	T	296;201;211;203	ENSP00000378611:I296T;ENSP00000378610:I201T;ENSP00000425589:I211T;ENSP00000264343:I203T	ENSP00000264343:I203T	I	+	2	0	0	ARHGAP24	87117827	87117827	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.040000	0.89188	2.272000	0.75746	0.460000	0.39030	ATC	0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.398	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	1	0	1		2	2	2	0		0	0	78		78	78	1	1.830000	-20.000000	1	0.520000	NM_031305			57	56		213	211	1		1	0		0	0	78	0		1.000000	2.024875e-01	0	0	0	4	0	57	213
NFKB1	4790	broad.mit.edu	37	4	103517377	103517377	+	Silent	SNP	A	A	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr4:103517377A>G	ENST00000505458.1	+	14	1657	c.1380A>G	c.(1378-1380)aaA>aaG	p.K460K	NFKB1_ENST00000600343.1_Silent_p.K280K|NFKB1_ENST00000226574.4_Silent_p.K461K|NFKB1_ENST00000394820.4_Silent_p.K460K			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	460	Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	TCTTTGGGAAAGTTATTGAAA	0.433																																						ENST00000505458.1	1.000000	6.200000e-01	9.000000e-01	7.000000e-01	0.790000	0.806740	0.790000	0.800000																										0				27						c.(1378-1380)aaA>aaG		nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)						73.0	75.0	75.0					4																	103517377		2203	4300	6503	SO:0001819	synonymous_variant	4790	0	0					g.chr4:103517377A>G	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1380A>G	chr4.hg19:g.103517377A>G		0					NFKB1_ENST00000226574.4_Silent_p.K461K|NFKB1_ENST00000600343.1_Silent_p.K280K|NFKB1_ENST00000394820.4_Silent_p.K460K	p.K460K			1	2	3	2.117417	P19838	NFKB1_HUMAN		14	1657	+		Hepatocellular(203;0.217)	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	1	1	hg19	c.1380A>G	CCDS54783.1	0																																																																																								0.522483		TCGA-2J-AABU-01A-11D-A40W-08	0.433	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1	1	0	1		2	2	2	0		0	0	68		68	68	1	1.830000	-20.000000	1	0.520000				59	58		226	223	1		1	1		0	0	68	0		1.000000	9.959273e-01	0	12	0	23	0	59	226
DNAH5	1767	broad.mit.edu	37	5	13871060	13871060	+	Missense_Mutation	SNP	A	A	G	rs112124692	byFrequency	TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr5:13871060A>G	ENST00000265104.4	-	24	3754	c.3650T>C	c.(3649-3651)aTt>aCt	p.I1217T	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1217	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTGGCGTCCAATGACAACCAT	0.383									Kartagener syndrome				A|||	11	0.00219649	0.0083	0.0	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0					ENST00000265104.4	1.000000	8.600000e-01	1	9.500000e-01	0.990000	0.984044	0.990000	1.000000																										0				378						c.(3649-3651)aTt>aCt		dynein, axonemal, heavy chain 5		A	THR/ILE	18,4388	24.3+/-50.5	0,18,2185	98.0	99.0	98.0		3650	4.7	0.0	5	dbSNP_132	98	0,8600		0,0,4300	yes	missense	DNAH5	NM_001369.2	89	0,18,6485	GG,GA,AA		0.0,0.4085,0.1384	benign	1217/4625	13871060	18,12988	2203	4300	6503	SO:0001583	missense	1767	64	121406	51	Kartagener syndrome	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	g.chr5:13871060A>G	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3650T>C	chr5.hg19:g.13871060A>G	ENSP00000265104:p.Ile1217Thr	1					CTB-51A17.1_ENST00000503244.1_RNA	p.I1217T	NM_001369.2	NP_001360.1	1	2	3	2.602165	Q8TE73	DYH5_HUMAN		24	3754	-	Lung NSC(4;0.00476)		Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	1	0	hg19	c.3650T>C	CCDS3882.1	1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	A	9.269	1.045083	0.19748	0.004085	0.0	ENSG00000039139	ENST00000265104	T	0.23754	1.89	5.84	4.68	0.58851	5.84	4.68	0.58851	.	0.318110	0.33515	N	0.004838	T	0.19805	0.0476	L	0.52573	1.65	0.09310	N	1	B	0.22480	0.07	B	0.27262	0.078	T	0.19549	-1.0302	10	0.72032	D	0.01	.	12.0386	0.53440	0.9326:0.0:0.0673:0.0	.	1217	Q8TE73	DYH5_HUMAN	T	1217	ENSP00000265104:I1217T	ENSP00000265104:I1217T	I	-	2	0	0	DNAH5	13924060	13924060	0.977000	0.34250	0.015000	0.15790	0.394000	0.30568	4.224000	0.58593	1.029000	0.39812	0.533000	0.62120	ATT	0.619048		TCGA-2J-AABU-01A-11D-A40W-08	0.383	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	1	0	1		2	2	2	0		0	0	77		77	77	1	1.830000	-3.049893	1	0.520000	NM_001369			92	92		331	326	1		1			0	0	77	0		1.000000	0	0	0	0	0	0	92	331
TMED9	54732	broad.mit.edu	37	5	177022351	177022351	+	Silent	SNP	C	C	T	rs370667269		TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr5:177022351C>T	ENST00000332598.6	+	5	699	c.642C>T	c.(640-642)ctC>ctT	p.L214L		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	214					COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCTCATCCTCGTGGCCATCG	0.592																																						ENST00000332598.6	1.000000	8.100000e-01	1	8.900000e-01	0.980000	0.958680	0.980000	1.000000																										0				10						c.(640-642)ctC>ctT		transmembrane emp24 protein transport domain containing 9							80.0	76.0	77.0					5																	177022351		2203	4300	6503	SO:0001819	synonymous_variant	54732	1	121412	38				g.chr5:177022351C>T	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.642C>T	chr5.hg19:g.177022351C>T		1						p.L214L	NM_017510.4	NP_059980.2	1	2	3	2.639433	Q9BVK6	TMED9_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	5	699	+	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Q14437|Q8WZ61	Silent	SNP	ENST00000332598.6	1	1	hg19	c.642C>T	CCDS4428.1	1																																																																																								0.619048		TCGA-2J-AABU-01A-11D-A40W-08	0.592	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	1	0	1		2	2	2	0		0	0	77		77	77	1	1.830000	-3.356083	1	0.520000	NM_017510			93	92		364	360	1		1	1		0	0	77	0		1.000000	1	0	113	0	448	0	93	364
F13A1	2162	broad.mit.edu	37	6	6225029	6225029	+	Missense_Mutation	SNP	A	A	G			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr6:6225029A>G	ENST00000264870.3	-	7	1128	c.863T>C	c.(862-864)gTc>gCc	p.V288A		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	288					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CGATGGGGGGACGCCATAGGC	0.507																																						ENST00000264870.3	0.970000	7.100000e-01	9.100000e-01	7.700000e-01	0.840000	0.846323	0.840000	0.850000																										0				62						c.(862-864)gTc>gCc		coagulation factor XIII, A1 polypeptide	L-Glutamine(DB00130)						110.0	104.0	106.0					6																	6225029		2203	4300	6503	SO:0001583	missense	2162	0	0					g.chr6:6225029A>G	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.863T>C	chr6.hg19:g.6225029A>G	ENSP00000264870:p.Val288Ala	1						p.V288A	NM_000129.3	NP_000120.2	0	1	1	1.537670	P00488	F13A_HUMAN		7	1128	-	Ovarian(93;0.0816)	all_hematologic(90;0.152)	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	1	1	hg19	c.863T>C	CCDS4496.1	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.43|15.43	2.832090|2.832090	0.50845|0.50845	.|.	.|.	ENSG00000124491|ENSG00000124491	ENST00000445223|ENST00000264870;ENST00000441301	.|D	.|0.96041	.|-3.89	5.51|5.51	5.51|5.51	0.81932|0.81932	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.065842	.|0.64402	.|D	.|0.000010	D|D	0.93390|0.93390	0.7892|0.7892	M|M	0.62209|0.62209	1.925|1.925	0.20489|0.20489	N|N	0.999891|0.999891	.|P;P	.|0.43788	.|0.66;0.817	.|B;P	.|0.47015	.|0.23;0.534	D|D	0.89821|0.89821	0.3989|0.3989	5|10	.|0.52906	.|T	.|0.07	.|.	14.8113|14.8113	0.69996|0.69996	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|225;288	.|F5H080;P00488	.|.;F13A_HUMAN	P|A	5|288;225	.|ENSP00000264870:V288A	.|ENSP00000264870:V288A	S|V	-|-	1|2	0|0	0|0	F13A1|F13A1	6170028|6170028	6170028|6170028	0.630000|0.630000	0.27155|0.27155	0.004000|0.004000	0.12327|0.12327	0.954000|0.954000	0.61252|0.61252	5.736000|5.736000	0.68597|0.68597	2.083000|2.083000	0.62718|0.62718	0.460000|0.460000	0.39030|0.39030	TCC|GTC	0.351351		TCGA-2J-AABU-01A-11D-A40W-08	0.507	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	1	0	1		2	2	2	0		0	0	105		105	103	1	1.830000	-20.000000	1	0.520000	NM_000129			104	103		244	243	1		1	0		0	0	105	0		1.000000	8.957314e-02	0	0	0	2	0	104	244
SLC35B3	51000	broad.mit.edu	37	6	8430252	8430252	+	Missense_Mutation	SNP	C	C	T	rs550117055		TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr6:8430252C>T	ENST00000379660.4	-	3	591	c.142G>A	c.(142-144)Gtg>Atg	p.V48M	SLC35B3_ENST00000339306.5_Missense_Mutation_p.V48M|SLC35B3_ENST00000426876.1_Missense_Mutation_p.V114M	NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	48					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					TTGGATGGCACAGTGATAGAA	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		17154	0.001		0.0	False		,,,				2504	0.0				Melanoma(83;700 1353 9357 11478 30548)	ENST00000379660.4	1.000000	8.000000e-01	9.800000e-01	8.700000e-01	0.930000	0.931929	0.930000	0.990000																										0				15						c.(142-144)Gtg>Atg		solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3							180.0	159.0	166.0					6																	8430252		2203	4300	6503	SO:0001583	missense	51000	1	121412	37				g.chr6:8430252C>T	AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"""Solute carriers"""	21601	protein-coding gene	gene with protein product	"""3' phosphoadenosine 5' phosphosulfate transporter 2"""	610845	"""chromosome 6 open reading frame 196"", ""solute carrier family 35, member B3"""	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.142G>A	chr6.hg19:g.8430252C>T	ENSP00000368981:p.Val48Met	1					SLC35B3_ENST00000339306.5_Missense_Mutation_p.V48M|SLC35B3_ENST00000426876.1_Missense_Mutation_p.V114M	p.V48M	NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	0	1	1	1.537670	Q9H1N7	S35B3_HUMAN		3	591	-	Ovarian(93;0.0569)		A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Missense_Mutation	SNP	ENST00000379660.4	1	1	hg19	c.142G>A	CCDS4508.1	1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537066	0.45176	.	.	ENSG00000124786	ENST00000379660;ENST00000339306;ENST00000426876	T;T	0.54071	1.23;0.59	5.88	4.09	0.47781	5.88	4.09	0.47781	.	0.219196	0.48286	N	0.000187	T	0.23572	0.0570	L	0.32530	0.975	0.45946	D	0.998777	P;B;B	0.51351	0.944;0.022;0.039	B;B;B	0.40825	0.341;0.014;0.014	T	0.03503	-1.1030	9	.	.	.	-9.0483	9.1897	0.37191	0.0:0.7267:0.0:0.2733	.	48;48;48	B4E2F5;Q9H1N7;B2R8V5	.;S35B3_HUMAN;.	M	48;48;114	ENSP00000368981:V48M;ENSP00000345902:V48M	.	V	-	1	0	0	SLC35B3	8375251	8375251	0.999000	0.42202	0.964000	0.40570	0.978000	0.69477	1.891000	0.39738	1.503000	0.48686	0.637000	0.83480	GTG	0.351351		TCGA-2J-AABU-01A-11D-A40W-08	0.378	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	1	0	1		2	2	2	0		0	0	136		136	134	1	1.830000	-20.000000	1	0.520000	NM_015948			89	88		166	166	1		1	1		0	0	136	0		1.000000	9.885574e-01	0	8	0	8	0	89	166
MLLT4	4301	broad.mit.edu	37	6	168315909	168315909	+	Silent	SNP	C	C	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr6:168315909C>A	ENST00000447894.2	+	18	2340	c.2340C>A	c.(2338-2340)gcC>gcA	p.A780A	MLLT4_ENST00000400822.3_Silent_p.A779A|MLLT4_ENST00000344191.4_Silent_p.A780A|MLLT4_ENST00000392108.3_Silent_p.A780A|MLLT4_ENST00000366806.2_Silent_p.A780A|MLLT4_ENST00000392112.1_Silent_p.A764A|MLLT4_ENST00000351017.4_Silent_p.A787A			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	780	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GAGTCAATGCCGCCCTGACCA	0.537			T	MLL	AL																																	ENST00000447894.2	0.120000	1.000000e-02	9.000000e-02	2.000000e-02	0.050000	0.061628	0.050000	0.050000				Dom	yes			Dom	yes		6	6q27	6q27	4301	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""				L	L	MLL		AL		0				65						c.(2338-2340)gcC>gcA		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4							140.0	109.0	120.0					6																	168315909		2203	4300	6503	SO:0001819	synonymous_variant	4301	0	0					g.chr6:168315909C>A	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2340C>A	chr6.hg19:g.168315909C>A		1					MLLT4_ENST00000392108.3_Silent_p.A780A|MLLT4_ENST00000351017.4_Silent_p.A787A|MLLT4_ENST00000392112.1_Silent_p.A764A|MLLT4_ENST00000344191.4_Silent_p.A780A|MLLT4_ENST00000400822.3_Silent_p.A779A|MLLT4_ENST00000366806.2_Silent_p.A780A	p.A780A			0	1	1	1.572129	P55196	AFAD_HUMAN		18	2340	+		Breast(66;1.07e-05)|Ovarian(120;0.024)	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	0	1	hg19	c.2340C>A		0																																																																																								0.351351		TCGA-2J-AABU-01A-11D-A40W-08	0.537	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	0	0	1		2	2	2	0		0	0	75		75	73	1	1.830000	-3.149900	1	0.520000	NM_005936			4	4		223	220	0		1	0		0	0	75	0		0.888002	8.937650e-02	0	0	0	22	0	4	223
IQCE	23288	broad.mit.edu	37	7	2617923	2617923	+	Silent	SNP	C	C	T			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr7:2617923C>T	ENST00000402050.2	+	7	697	c.513C>T	c.(511-513)ctC>ctT	p.L171L	IQCE_ENST00000438376.2_Silent_p.L155L|IQCE_ENST00000404984.1_Silent_p.L120L|IQCE_ENST00000325979.7_Silent_p.L106L	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	171						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		GAACGAAGCTCCGGCGCCTGG	0.612																																						ENST00000402050.2	1.000000	7.400000e-01	1	8.300000e-01	0.930000	0.922025	0.930000	1.000000																										0				30						c.(511-513)ctC>ctT		IQ motif containing E							65.0	75.0	72.0					7																	2617923		2146	4247	6393	SO:0001819	synonymous_variant	23288	0	0					g.chr7:2617923C>T	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.513C>T	chr7.hg19:g.2617923C>T		0					IQCE_ENST00000438376.2_Silent_p.L155L|IQCE_ENST00000404984.1_Silent_p.L120L|IQCE_ENST00000325979.7_Silent_p.L106L	p.L171L	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	1	2	3	2.101156	Q6IPM2	IQCE_HUMAN		7	697	+		Ovarian(82;0.0112)	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	1	1	hg19	c.513C>T	CCDS43542.1	1																																																																																								0.521245		TCGA-2J-AABU-01A-11D-A40W-08	0.612	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	1	0	1		2	2	2	0		0	0	54		54	54	1	1.830000	-4.719676	1	0.520000	NM_152558			65	64		203	198	1		1	1		0	0	54	0		1.000000	7.854974e-01	0	2	0	9	0	65	203
PMS2	5395	broad.mit.edu	37	7	6043387	6043387	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr7:6043387G>A	ENST00000265849.7	-	4	392	c.287C>T	c.(286-288)gCc>gTc	p.A96V	Y_RNA_ENST00000365120.1_RNA|PMS2_ENST00000382321.4_Missense_Mutation_p.A96V|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.A96V|PMS2_ENST00000441476.2_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	96					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		AGTTAGGTCGGCAAACTCTTG	0.403			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													ENST00000265849.7	0.170000	2.000000e-02	1.200000e-01	4.000000e-02	0.070000	0.087338	0.070000	0.080000			yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	yes	Rec		Hereditary non-polyposis colorectal cancer, Turcot syndrome	7	7p22	7p22	5395	Mis, N, F	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)				E	E		colorectal, endometrial, ovarian, medulloblastoma, glioma			0				46						c.(286-288)gCc>gTc	Direct reversal of damage;Mismatch excision repair (MMR)	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)							55.0	62.0	60.0					7																	6043387		1424	2456	3880	SO:0001583	missense	5395	0	0		Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	g.chr7:6043387G>A		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.287C>T	chr7.hg19:g.6043387G>A	ENSP00000265849:p.Ala96Val	0					Y_RNA_ENST00000365120.1_RNA|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.A96V|PMS2_ENST00000382321.4_Missense_Mutation_p.A96V|PMS2_ENST00000441476.2_Intron	p.A96V	NM_000535.5	NP_000526	1	2	3	2.101156	P54278	PMS2_HUMAN		4	392	-		Ovarian(82;0.0694)	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	0	1	hg19	c.287C>T	CCDS5343.1	0	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760290	0.49468	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000382321;ENST00000406569	T;T;T	0.74421	-0.84;-0.84;-0.84	5.68	4.8	0.61643	5.68	4.8	0.61643	DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.181750	0.48767	D	0.000165	T	0.68467	0.3004	L	0.45698	1.435	0.80722	D	1	B;P;P	0.49447	0.025;0.924;0.493	B;B;B	0.40677	0.003;0.337;0.12	T	0.67229	-0.5723	10	0.27082	T	0.32	-5.7265	16.7528	0.85490	0.0:0.1292:0.8708:0.0	.	96;96;96	P54278-3;P54278-2;P54278	.;.;PMS2_HUMAN	V	96;49;96;96	ENSP00000265849:A96V;ENSP00000371758:A96V;ENSP00000384308:A96V	ENSP00000265849:A96V	A	-	2	0	0	PMS2	6009913	6009913	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	6.309000	0.72825	1.383000	0.46405	0.484000	0.47621	GCC	0.521245		TCGA-2J-AABU-01A-11D-A40W-08	0.403	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	0	0	1		2	2	6	0		0	0	74		74	74	1	1.830000	-2.536141	1	0.520000	NM_000535			5	5		257	251	0		1	0	0	0	1	74	498		0.934263	1.764918e-03	8.743420e-01	0	0	3	518	5	257
ELMO1	9844	broad.mit.edu	37	7	37382282	37382282	+	Missense_Mutation	SNP	C	C	T	rs146510671		TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr7:37382282C>T	ENST00000310758.4	-	2	660	c.13G>A	c.(13-15)Gcg>Acg	p.A5T	ELMO1_ENST00000448602.1_Missense_Mutation_p.A5T|ELMO1_ENST00000442504.1_Missense_Mutation_p.A5T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	5					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)	p.A5T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						ACGATGTCCGCGGGTGGCGGC	0.502																																						ENST00000310758.4	1.000000	8.900000e-01	1	9.600000e-01	0.990000	0.987705	0.990000	1.000000																										1	Substitution - Missense(1)	p.A5T(1)	ovary(1)	58						c.(13-15)Gcg>Acg		engulfment and cell motility 1		C	THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	116.0	121.0	119.0		13,13,13	4.0	0.0	7	dbSNP_134	119	0,8600		0,0,4300	no	missense,missense,missense	ELMO1	NM_001206480.1,NM_001206482.1,NM_014800.10	58,58,58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign,benign	5/728,5/728,5/728	37382282	2,13004	2203	4300	6503	SO:0001583	missense	9844	5	121408	42				g.chr7:37382282C>T	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"""Engulfment and cell motility proteins"""	16286	protein-coding gene	gene with protein product		606420	"""engulfment and cell motility 1 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.13G>A	chr7.hg19:g.37382282C>T	ENSP00000312185:p.Ala5Thr	0					ELMO1_ENST00000442504.1_Missense_Mutation_p.A5T|ELMO1_ENST00000448602.1_Missense_Mutation_p.A5T	p.A5T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	1	2	3	2.101156	Q92556	ELMO1_HUMAN		2	660	-			A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	1	1	hg19	c.13G>A	CCDS5449.1	1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.533964	0.64972	4.54E-4	0.0	ENSG00000155849	ENST00000310758;ENST00000442504;ENST00000448602;ENST00000455119;ENST00000455879;ENST00000453399;ENST00000445322	T;T;T;T;T;T;T	0.44881	2.53;2.53;2.53;1.53;1.52;0.94;0.91	4.94	4.03	0.46877	4.94	4.03	0.46877	.	0.200167	0.41823	D	0.000804	T	0.27594	0.0678	N	0.19112	0.55	0.44323	D	0.997201	B	0.14012	0.009	B	0.14578	0.011	T	0.04635	-1.0937	10	0.25106	T	0.35	.	12.5184	0.56046	0.1731:0.8269:0.0:0.0	.	5	Q92556	ELMO1_HUMAN	T	5	ENSP00000312185:A5T;ENSP00000406952:A5T;ENSP00000394458:A5T;ENSP00000406610:A5T;ENSP00000416090:A5T;ENSP00000391734:A5T;ENSP00000397857:A5T	ENSP00000312185:A5T	A	-	1	0	0	ELMO1	37348807	37348807	0.961000	0.32948	0.033000	0.17914	0.945000	0.59286	2.373000	0.44266	1.166000	0.42689	0.655000	0.94253	GCG	0.521245		TCGA-2J-AABU-01A-11D-A40W-08	0.502	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	1	0	1		2	2	2	0		0	0	149		149	148	1	1.830000	-20.000000	1	0.520000	NM_130442			153	151		414	407	1		1	0		0	0	149	0		1.000000	7.359788e-02	0	0	0	2	0	153	414
PXDNL	137902	broad.mit.edu	37	8	52321490	52321490	+	Silent	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr8:52321490G>A	ENST00000356297.4	-	17	2794	c.2694C>T	c.(2692-2694)aaC>aaT	p.N898N	PXDNL_ENST00000543296.1_Silent_p.N898N	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	898					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TCCCGTAAACGTTGGAGCCAT	0.622																																						ENST00000356297.4	1.000000	8.500000e-01	1	9.400000e-01	0.990000	0.981007	0.990000	1.000000																										0				48						c.(2692-2694)aaC>aaT		peroxidasin homolog (Drosophila)-like							43.0	48.0	46.0					8																	52321490		2017	4166	6183	SO:0001819	synonymous_variant	137902	0	0					g.chr8:52321490G>A		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2694C>T	chr8.hg19:g.52321490G>A		0					PXDNL_ENST00000543296.1_Silent_p.N898N	p.N898N	NM_144651.4	NP_653252	1	2	3	2.108206	A1KZ92	PXDNL_HUMAN		17	2794	-		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	1	1	hg19	c.2694C>T	CCDS47855.1	1	.	.	.	.	.	.	.	.	.	.	G	0.096	-1.159576	0.01686	.	.	ENSG00000147485	ENST00000522933	.	.	.	4.01	-2.84	0.05751	4.01	-2.84	0.05751	.	.	.	.	.	T	0.47154	0.1430	.	.	.	0.51482	D	0.999926	.	.	.	.	.	.	T	0.38714	-0.9648	4	.	.	.	.	4.4763	0.11745	0.6029:0.0:0.2268:0.1703	.	.	.	.	M	17	.	.	T	-	2	0	0	PXDNL	52484043	52484043	0.178000	0.23122	0.000000	0.03702	0.005000	0.04900	-0.180000	0.09754	-0.477000	0.06832	0.655000	0.94253	ACG	0.521245		TCGA-2J-AABU-01A-11D-A40W-08	0.622	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	1	0	1		2	2	2	0		0	0	69		69	67	1	1.830000	-20.000000	1	0.520000	NM_144651			74	72		197	197	1		1			0	0	69	0		1.000000	0	0	0	0	0	0	74	197
DENND4C	55667	broad.mit.edu	37	9	19305370	19305370	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr9:19305370G>A	ENST00000380432.2	+	6	657	c.624G>A	c.(622-624)tgG>tgA	p.W208*	DENND4C_ENST00000602925.1_Nonsense_Mutation_p.W444*|DENND4C_ENST00000434457.2_Nonsense_Mutation_p.W444*			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	208	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CATTTCAGTGGCAATGCCCAT	0.328																																						ENST00000380432.2	0.080000	0	6.000000e-02	1.000000e-02	0.030000	0.040957	0.030000	0.040000																										0				40						c.(622-624)tgG>tgA		DENN/MADD domain containing 4C							167.0	163.0	164.0					9																	19305370		2203	4300	6503	SO:0001587	stop_gained	55667	0	0					g.chr9:19305370G>A	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.624G>A	chr9.hg19:g.19305370G>A	ENSP00000369797:p.Trp208*	1					DENND4C_ENST00000602925.1_Nonsense_Mutation_p.W444*|DENND4C_ENST00000434457.2_Nonsense_Mutation_p.W444*	p.W208*			0	1	1	1.541911	Q5VZ89	DEN4C_HUMAN		6	657	+			A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Nonsense_Mutation	SNP	ENST00000380432.2	0	1	hg19	c.624G>A		0	.	.	.	.	.	.	.	.	.	.	G	36	5.966709	0.97156	.	.	ENSG00000137145	ENST00000380437	.	.	.	4.71	4.71	0.59529	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5753	17.8373	0.88701	0.0:0.0:1.0:0.0	.	.	.	.	X	208	.	ENSP00000369802:W208X	W	+	3	0	0	DENND4C	19295370	19295370	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.407000	0.97325	2.441000	0.82636	0.585000	0.79938	TGG	0.351351		TCGA-2J-AABU-01A-11D-A40W-08	0.328	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		0	0	1		2	2	2	0		0	0	169		169	168	1	1.830000	-2.282842	0	0.520000	NM_017925			5	5		408	406	0		1	0		0	0	169	0		0.937102	2.432808e-04	0	0	0	2	0	5	408
PIGO	84720	broad.mit.edu	37	9	35090660	35090660	+	Missense_Mutation	SNP	G	G	A			TCGA-2J-AABU-01A-11D-A40W-08	TCGA-2J-AABU-10A-01D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2f137e1d-fdcc-4d47-84e4-6fb48a7f236b	39946151-48c1-482f-961e-3f170e963b75	g.chr9:35090660G>A	ENST00000378617.3	-	8	3051	c.2657C>T	c.(2656-2658)aCt>aTt	p.T886I	PIGO_ENST00000341666.3_Missense_Mutation_p.T886I|PIGO_ENST00000298004.5_Missense_Mutation_p.T469I|PIGO_ENST00000361778.2_Missense_Mutation_p.T469I	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	886				PFTVPWQAVSAWALMATQTFYSTGHQPVFPAIHWHAAFVGF PEGHGSCTWLPALLVGANTFASHLLFAVGCPLLLLWPFLCE SQGL -> KYLSSDSLKDNSDVSSAPLVFKEVLLLMFLSLT EGPMPHTTRKVFLVSSLLPAIAKQIDPSCWFPGFMERRDKE SSKTPCGNAASS (in Ref. 8; BAB89338). {ECO:0000305}.	C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCATGGCACAGTAAAAGGACC	0.502																																						ENST00000378617.3	0.310000	3.000000e-02	2.400000e-01	8.000000e-02	0.150000	0.169784	0.150000	0.160000																										0				38						c.(2656-2658)aCt>aTt		phosphatidylinositol glycan anchor biosynthesis, class O							54.0	53.0	54.0					9																	35090660		2203	4300	6503	SO:0001583	missense	84720	0	0					g.chr9:35090660G>A	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.2657C>T	chr9.hg19:g.35090660G>A	ENSP00000367880:p.Thr886Ile	1					PIGO_ENST00000298004.5_Missense_Mutation_p.T469I|PIGO_ENST00000341666.3_Missense_Mutation_p.T886I|PIGO_ENST00000361778.2_Missense_Mutation_p.T469I	p.T886I	NM_032634.3	NP_116023.2	1	15	16	10.043740	Q8TEQ8	PIGO_HUMAN	LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)	8	3051	-			B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Missense_Mutation	SNP	ENST00000378617.3	0	1	hg19	c.2657C>T	CCDS6575.1	0	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931790	0.34096	.	.	ENSG00000165282	ENST00000298004;ENST00000378617;ENST00000341666;ENST00000361778	T;T;T;T	0.55930	0.5;0.49;0.49;0.5	5.18	4.29	0.51040	5.18	4.29	0.51040	.	0.358601	0.29205	N	0.012826	T	0.34337	0.0894	N	0.14661	0.345	0.18873	N	0.999982	B;B	0.16802	0.019;0.005	B;B	0.17433	0.018;0.005	T	0.14559	-1.0468	10	0.22109	T	0.4	-16.9499	12.8394	0.57793	0.078:0.0:0.922:0.0	.	469;886	Q8TEQ8-2;Q8TEQ8	.;PIGO_HUMAN	I	469;886;886;469	ENSP00000298004:T469I;ENSP00000367880:T886I;ENSP00000339382:T886I;ENSP00000354678:T469I	ENSP00000298004:T469I	T	-	2	0	0	PIGO	35080660	35080660	0.683000	0.27633	1.000000	0.80357	0.995000	0.86356	0.434000	0.21494	1.424000	0.47217	0.655000	0.94253	ACT	0.896552		TCGA-2J-AABU-01A-11D-A40W-08	0.502	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	0	0	1		2	2	2	0		0	0	40		40	36	1	1.830000	-4.927041	1	0.520000	NM_032634			8	7		912	827	0		1	0		0	0	40	0		0.984299	8.297407e-01	0	0	0	370	0	8	912
