#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
INF2	64423	broad.mit.edu	37	14	105180688	105180689	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			-	T	-	-		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr14:105180688_105180689insT	ENST00000392634.4	+	21	3301_3302	c.3189_3190insT	c.(3190-3192)ttgfs	p.L1064fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.L1064fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1064					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CCCTGGAGCAGTTGGAGGAGGG	0.663																																						ENST00000392634.4	0.730000	2.500000e-01	0.610000	0.340000	0.460000	0.482168	0.460000	0.460000																										0				8						c.(3190-3192)ttgfs		inverted formin, FH2 and WH2 domain containing																																				SO:0001589	frameshift_variant	64423	0	0					g.chr14:105180688_105180689insT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3191dupT	chr14.hg19:g.105180690_105180690dupT	ENSP00000376410:p.Leu1064fs	1					INF2_ENST00000330634.7_Frame_Shift_Ins_p.L1064fs	p.L1064fs	NM_022489.3	NP_071934.3	0	1	1	1.546377	Q27J81	INF2_HUMAN	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	21	3301_3302	+		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	0	1	hg19	c.3189_3190insT	CCDS9989.2	0																																																																																								0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.663	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	1	0	1		2	2		0	0	0	0	33	0	33	34	1	1.800000	-19.620090	1	0.560000	NM_022489		0	10	9	0	45	42	0	0	1	0		0	0	33	0	0	0.996711	1		0	0	245	0	10	45
MBD1	4152	broad.mit.edu	37	18	47797907	47797914	+	Splice_Site	DEL	GGACCTAG	GGACCTAG	-	rs371943213		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			GGACCTAG	-	GGACCTAG	GGACCTAG		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr18:47797907_47797914delGGACCTAG	ENST00000591416.1	-	16	2210_2213	c.1779_1782delCTAGGTCC	c.(1777-1782)agctag>ag	p.S*593fs	MBD1_ENST00000353909.3_Splice_Site_p.S*544fs|MBD1_ENST00000349085.2_Splice_Site_p.S*491fs|MBD1_ENST00000382948.5_Splice_Site_p.S*593fs|MBD1_ENST00000269468.5_Splice_Site_p.S*593fs|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000436910.1_Splice_Site_p.S*524fs|MBD1_ENST00000457839.2_Splice_Site_p.S*618fs|MBD1_ENST00000398493.1_Splice_Site_p.S*537fs|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000585595.1_Splice_Site_p.S*618fs|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000347968.3_Splice_Site_p.S*537fs|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000591535.1_Splice_Site_p.S*524fs|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000398495.2_Splice_Site_p.S*554fs|MBD1_ENST00000424334.2_Splice_Site_p.S*644fs|MBD1_ENST00000398488.1_Splice_Site_p.S*491fs			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	593					negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						TAAGGTCTTTGGACCTAGGGAAAAGGGA	0.442																																						ENST00000591416.1	0.600000	4.200000e-01	0.560000	0.460000	0.510000	0.516442	0.510000	0.510000																										0				36						c.(1777-1782)agctag>ag		methyl-CpG binding domain protein 1																																				SO:0001630	splice_region_variant	4152	0	0					g.chr18:47797907_47797914delGGACCTAG	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.1779-1CTAGGTCC>-	chr18.hg19:g.47797907_47797914delGGACCTAG		1					MBD1_ENST00000349085.2_Splice_Site_p.S*491fs|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000353909.3_Splice_Site_p.S*544fs|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000398488.1_Splice_Site_p.S*491fs|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000398493.1_Splice_Site_p.S*537fs|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000347968.3_Splice_Site_p.S*537fs|MBD1_ENST00000585595.1_Splice_Site_p.S*618fs|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000457839.2_Splice_Site_p.S*618fs|MBD1_ENST00000591535.1_Splice_Site_p.S*524fs|MBD1_ENST00000382948.5_Splice_Site_p.S*593fs|MBD1_ENST00000436910.1_Splice_Site_p.S*524fs|MBD1_ENST00000269468.5_Splice_Site_p.S*593fs|MBD1_ENST00000424334.2_Splice_Site_p.S*644fs|MBD1_ENST00000398495.2_Splice_Site_p.S*554fs	p.S*593fs			0	1	1	1.553807	Q9UIS9	MBD1_HUMAN		16	2210_2213	-			A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Splice_Site	DEL	ENST00000591416.1	1	1	hg19	c.1779_1782delCTAGGTCC	CCDS11943.1	0																																																																																								0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.442	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	0	0	1		69	2		0	0	0	28	355	0	355	374	1	1.800000	-20.000000	1	0.560000	NM_015846	Frame_Shift_Del	0	115	208	0	459	519	0	0	1	0		0	0	355	0	0	1.000000	9.997315e-01		0	0	50	0	115	459
SMAD4	4089	broad.mit.edu	37	18	48586256	48586262	+	Frame_Shift_Del	DEL	GCATTCC	GCATTCC	-	rs369088915		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			GCATTCC	-	GCATTCC	GCATTCC		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr18:48586256_48586262delGCATTCC	ENST00000342988.3	+	8	1463_1469	c.925_931delGCATTCC	c.(925-933)gcattccagfs	p.AFQ309fs	SMAD4_ENST00000398417.2_Frame_Shift_Del_p.AFQ309fs|SMAD4_ENST00000588745.1_Intron	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	309	SAD.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)|p.Q311*(2)|p.F310L(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CAATGAGCTTGCATTCCAGCCTCCCAT	0.329																																						ENST00000342988.3	0.590000	3.600000e-01	0.530000	0.410000	0.470000	0.478078	0.470000	0.470000																										42	Whole gene deletion(36)|Unknown(3)|Substitution - Nonsense(2)|Substitution - Missense(1)	p.0?(36)|p.?(3)|p.Q311*(2)|p.F310L(1)	pancreas(27)|large_intestine(4)|breast(4)|stomach(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	454	GRCh37	CI064731	SMAD4	I		c.(925-933)gcattccagfs		SMAD family member 4																																				SO:0001589	frameshift_variant	4089	0	0					g.chr18:48586256_48586262delGCATTCC	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.925_931delGCATTCC	chr18.hg19:g.48586256_48586262delGCATTCC	ENSP00000341551:p.Ala309fs	1					SMAD4_ENST00000588745.1_Intron|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.AFQ309fs	p.AFQ309fs	NM_005359.5	NP_005350.1	0	1	1	1.553807	Q13485	SMAD4_HUMAN		8	1463_1469	+		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)	A8K405	Frame_Shift_Del	DEL	ENST00000342988.3	1	1	hg19	c.925_931delGCATTCC	CCDS11950.1	0																																																																																								0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.329	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	1		8	2	2	0	0	0	1	177	0	177	177	1	1.800000	-20.000000	1	0.560000	NM_005359		0	56	66	0	247	242	0	0	1	0	1	0	0	177	692	0	1.000000	9.971798e-01	1	1	95	41	607	56	247
SHOC2	8036	broad.mit.edu	37	10	112724158	112724158	+	Silent	SNP	A	A	G			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr10:112724158A>G	ENST00000369452.4	+	2	387	c.42A>G	c.(40-42)aaA>aaG	p.K14K	SHOC2_ENST00000265277.5_Silent_p.K14K|SHOC2_ENST00000489390.1_Intron	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	14					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		CTAAAGAAAAAGATCCCAAAG	0.383																																						ENST00000369452.4	1.000000	2.000000e-02	0.160000	0.050000	0.090000	0.136499	0.090000	0.080000																										0				17						c.(40-42)aaA>aaG		soc-2 suppressor of clear homolog (C. elegans)							47.0	51.0	50.0					10																	112724158		2202	4299	6501	SO:0001819	synonymous_variant	8036	0	0					g.chr10:112724158A>G	AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"""soc-2 (suppressor of clear, C.elegans) homolog"""			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.42A>G	chr10.hg19:g.112724158A>G		0					SHOC2_ENST00000265277.5_Silent_p.K14K|SHOC2_ENST00000489390.1_Intron	p.K14K	NM_007373.3	NP_031399.2	1	2	3	2.169384	Q9UQ13	SHOC2_HUMAN		2	387	+			A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Silent	SNP	ENST00000369452.4	0	1	hg19	c.42A>G	CCDS7568.1	0																																																																																								0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.383	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	0	0	1	2	2	2	2	0	0	0	0	106	106	106	106	1	1.800000	-3.183656	1	0.560000	NM_007373		0	4	4	0	170	165	0		1	0		0	0	106	0	0	0.884373	2.699243e-01	0	0	0	36	0	4	170
TDRD1	56165	broad.mit.edu	37	10	115970681	115970681	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr10:115970681G>T	ENST00000369280.1	+	13	2075	c.1615G>T	c.(1615-1617)Gat>Tat	p.D539Y	TDRD1_ENST00000251864.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000369281.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000422662.1_Missense_Mutation_p.D200Y|TDRD1_ENST00000369282.1_Missense_Mutation_p.D539Y			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	539					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TCCACGCTCTGATTTTTATCC	0.348																																						ENST00000369280.1	1.000000	8.200000e-01	1.000000	0.910000	0.990000	0.968727	0.990000	1.000000																										0				48						c.(1615-1617)Gat>Tat		tudor domain containing 1							120.0	108.0	112.0					10																	115970681		2203	4300	6503	SO:0001583	missense	56165	0	0					g.chr10:115970681G>T	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"""Tudor domain containing"""	11712	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.1"""	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.1615G>T	chr10.hg19:g.115970681G>T	ENSP00000358286:p.Asp539Tyr	0					TDRD1_ENST00000369281.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000369282.1_Missense_Mutation_p.D539Y|TDRD1_ENST00000251864.2_Missense_Mutation_p.D539Y|TDRD1_ENST00000422662.1_Missense_Mutation_p.D200Y	p.D539Y			1	2	3	2.169384	Q9BXT4	TDRD1_HUMAN		13	2075	+		Colorectal(252;0.172)|Breast(234;0.188)	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	1	1	hg19	c.1615G>T		1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356797	0.41801	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	T;T;T;T;T	0.09723	2.95;2.95;2.95;2.95;2.95	5.9	4.05	0.47172	5.9	4.05	0.47172	Maternal tudor protein (1);	0.205916	0.39985	N	0.001202	T	0.27098	0.0664	M	0.75884	2.315	0.09310	N	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.81914	0.978;0.973;0.995;0.955;0.991	T	0.07366	-1.0776	10	0.66056	D	0.02	-14.3001	5.4576	0.16600	0.2129:0.0:0.6388:0.1482	.	200;539;539;539;539	Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	.;TDRD1_HUMAN;.;.;.	Y	539;539;539;200;539	ENSP00000358288:D539Y;ENSP00000251864:D539Y;ENSP00000358287:D539Y;ENSP00000402794:D200Y;ENSP00000358286:D539Y	ENSP00000251864:D539Y	D	+	1	0	0	TDRD1	115960671	115960671	0.914000	0.31030	0.540000	0.28089	0.698000	0.40448	1.437000	0.34991	1.498000	0.48600	0.563000	0.77884	GAT	0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.348	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2	0	0	0	2	2	2	2	0	0	0	0	123	123	123	122	1	1.800000	-6.472448	1	0.560000			0	77	75	0	199	196	1		1			0	0	123	0	0	1.000000	0	0	0	0	0	0	77	199
HKDC1	80201	broad.mit.edu	37	10	71005968	71005968	+	Missense_Mutation	SNP	C	C	T	rs148723879		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr10:71005968C>T	ENST00000354624.5	+	8	1142	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	HKDC1_ENST00000395086.2_Missense_Mutation_p.R337W	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	337	Hexokinase type-2 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GATCGAAACACGGCACGTGGC	0.572																																						ENST00000354624.5	1.000000	7.900000e-01	1.000000	0.880000	0.980000	0.955245	0.980000	1.000000																										0				34						c.(1009-1011)Cgg>Tgg		hexokinase domain containing 1		C	TRP/ARG	0,4406		0,0,2203	117.0	100.0	106.0		1009	2.7	0.7	10	dbSNP_134	106	2,8598	2.2+/-6.3	0,2,4298	no	missense	HKDC1	NM_025130.3	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	337/918	71005968	2,13004	2203	4300	6503	SO:0001583	missense	80201	11	121412	41				g.chr10:71005968C>T		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1009C>T	chr10.hg19:g.71005968C>T	ENSP00000346643:p.Arg337Trp	0					HKDC1_ENST00000395086.2_Missense_Mutation_p.R337W	p.R337W	NM_025130.3	NP_079406	1	2	3	2.169384	Q2TB90	HKDC1_HUMAN		8	1142	+			B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	1	1	hg19	c.1009C>T	CCDS7288.1	1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.900111	0.52227	0.0	2.33E-4	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.96554	-4.05;-4.05	4.68	2.69	0.31865	4.68	2.69	0.31865	Hexokinase, C-terminal (1);	0.498975	0.22141	N	0.064050	D	0.93716	0.7992	M	0.63843	1.955	0.09310	N	1	D	0.69078	0.997	B	0.41917	0.37	D	0.88588	0.3141	10	0.87932	D	0	-9.0294	8.3136	0.32086	0.3743:0.5092:0.1165:0.0	.	337	Q2TB90	HKDC1_HUMAN	W	337	ENSP00000346643:R337W;ENSP00000378521:R337W	ENSP00000346643:R337W	R	+	1	2	2	HKDC1	70675974	70675974	0.065000	0.20965	0.684000	0.30055	0.622000	0.37654	2.558000	0.45879	1.172000	0.42781	0.561000	0.74099	CGG	0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.572	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	1	0	1	2	2	2	2	0	0	0	0	130	130	130	126	1	1.800000	-20.000000	1	0.560000	NM_025130		0	73	72	0	196	192	1		1	1		0	0	130	0	0	1.000000	1	0	23	0	64	0	73	196
SLIT1	6585	broad.mit.edu	37	10	98762035	98762035	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr10:98762035C>T	ENST00000266058.4	-	36	4491	c.4246G>A	c.(4246-4248)Ggg>Agg	p.G1416R	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Intron	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	1416					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GCCAGGGCCCCGGCCTGGTTG	0.662																																						ENST00000266058.4	1.000000	6.000000e-01	1.000000	0.760000	0.960000	0.905226	0.960000	1.000000																										0				78						c.(4246-4248)Ggg>Agg		slit homolog 1 (Drosophila)							13.0	15.0	14.0					10																	98762035		2199	4289	6488	SO:0001583	missense	6585	1	121164	23				g.chr10:98762035C>T	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.4246G>A	chr10.hg19:g.98762035C>T	ENSP00000266058:p.Gly1416Arg	0					ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Intron	p.G1416R	NM_003061.2	NP_003052.2	1	2	3	2.169384	O75093	SLIT1_HUMAN		36	4491	-		Colorectal(252;0.162)	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	1	1	hg19	c.4246G>A	CCDS7453.1	1	.	.	.	.	.	.	.	.	.	.	C	4.285	0.052094	0.08291	.	.	ENSG00000187122	ENST00000266058	T	0.80480	-1.38	4.42	2.57	0.30868	4.42	2.57	0.30868	.	0.164002	0.53938	N	0.000048	T	0.58323	0.2114	N	0.04203	-0.255	0.45354	D	0.998344	B	0.06786	0.001	B	0.04013	0.001	T	0.45804	-0.9236	10	0.29301	T	0.29	.	10.0301	0.42096	0.0:0.771:0.0:0.229	.	1416	O75093	SLIT1_HUMAN	R	1416	ENSP00000266058:G1416R	ENSP00000266058:G1416R	G	-	1	0	0	SLIT1	98752025	98752025	0.007000	0.16637	0.178000	0.23040	0.155000	0.21991	0.849000	0.27723	0.499000	0.27970	-0.221000	0.12465	GGG	0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.662	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	1	0	1	2	2	2	2	0	0	0	0	28	28	28	28	1	1.800000	-20.000000	1	0.560000	NM_003061		0	16	16	0	45	44	1		1	0		0	0	28	0	0	0.999969	7.589286e-02	0	0	0	2	0	16	45
GFRA1	2674	broad.mit.edu	37	10	118030528	118030528	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr10:118030528C>T	ENST00000355422.6	-	3	690	c.140G>A	c.(139-141)cGc>cAc	p.R47H	GFRA1_ENST00000439649.3_Missense_Mutation_p.R47H|GFRA1_ENST00000490345.1_5'Flank|GFRA1_ENST00000369236.1_Missense_Mutation_p.R47H	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	47					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		CCTTAGCGTGCGGTACTTGGT	0.637																																					Ovarian(128;329 1725 45498 46808 50759)	ENST00000355422.6	1.000000	3.000000e-02	0.140000	0.060000	0.090000	0.135162	0.090000	0.090000																										0				26						c.(139-141)cGc>cAc		GDNF family receptor alpha 1							71.0	59.0	63.0					10																	118030528		2203	4300	6503	SO:0001583	missense	2674	0	0					g.chr10:118030528C>T	AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.140G>A	chr10.hg19:g.118030528C>T	ENSP00000347591:p.Arg47His	0					GFRA1_ENST00000369236.1_Missense_Mutation_p.R47H|GFRA1_ENST00000439649.3_Missense_Mutation_p.R47H|GFRA1_ENST00000490345.1_5'Flank	p.R47H	NM_005264.4	NP_005255.1	1	2	3	2.169384	P56159	GFRA1_HUMAN		3	690	-		Lung NSC(174;0.21)	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	0	1	hg19	c.140G>A	CCDS44481.1	0	.	.	.	.	.	.	.	.	.	.	C	35	5.527077	0.96431	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000369234	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	3.95	3.95	0.45737	3.95	3.95	0.45737	GDNF/GAS1 (2);	0.000000	0.85682	D	0.000000	T	0.76190	0.3953	L	0.61036	1.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.78682	-0.2109	10	0.52906	T	0.07	-20.05	16.2431	0.82426	0.0:1.0:0.0:0.0	.	47;47	P56159;P56159-2	GFRA1_HUMAN;.	H	47	ENSP00000393725:R47H;ENSP00000358239:R47H;ENSP00000347591:R47H;ENSP00000358237:R47H	ENSP00000347591:R47H	R	-	2	0	0	GFRA1	118020518	118020518	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.617000	0.83032	2.044000	0.60594	0.549000	0.68633	CGC	0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.637	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	0	0	1	2	2	2	2	0	0	0	0	134	134	134	134	1	1.800000	-3.567326	1	0.560000	NM_145793		0	7	7	0	277	275	0		1	0		0	0	134	0	0	0.980472	8.179766e-03	0	0	0	5	0	7	277
HINFP	25988	broad.mit.edu	37	11	119004822	119004822	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr11:119004822C>T	ENST00000350777.2	+	10	1231	c.1168C>T	c.(1168-1170)Cgg>Tgg	p.R390W	HINFP_ENST00000527410.1_Silent_p.C410C	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	390	Interaction with NPAT.|Required for activation of histone H4 transcription and contributes to DNA- binding.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.R390W(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TGGCTATATGCGGCTGCAGCT	0.567											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000350777.2	0.130000	1.000000e-02	0.090000	0.030000	0.050000	0.064355	0.050000	0.060000																										1	Substitution - Missense(1)	p.R390W(1)	kidney(1)	23						c.(1168-1170)Cgg>Tgg		histone H4 transcription factor							58.0	59.0	59.0					11																	119004822		2200	4295	6495	SO:0001583	missense	25988	0	0					g.chr11:119004822C>T	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1168C>T	chr11.hg19:g.119004822C>T	ENSP00000318085:p.Arg390Trp	0		OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1492	HINFP_ENST00000527410.1_Silent_p.C410C	p.R390W	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	1	2	3	2.138887	Q9BQA5	HINFP_HUMAN		10	1231	+			B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	0	1	hg19	c.1168C>T	CCDS8414.1	0	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964717	0.74131	.	.	ENSG00000172273	ENST00000350777	T	0.10573	2.86	5.31	2.36	0.29203	5.31	2.36	0.29203	.	0.000000	0.85682	D	0.000000	T	0.29458	0.0734	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02646	-1.1129	10	0.87932	D	0	-27.7523	14.9379	0.70970	0.5073:0.4927:0.0:0.0	.	390	Q9BQA5	HINFP_HUMAN	W	390	ENSP00000318085:R390W	ENSP00000318085:R390W	R	+	1	2	2	HINFP	118510032	118510032	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.333000	0.43912	0.360000	0.24265	-0.152000	0.13540	CGG	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.567	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	0	0	1	2	2	2	2	0	0	0	0	188	188	188	187	1	1.800000	-2.500008	1	0.560000	NM_015517		0	5	5	0	326	321	0		1	0		0	0	188	0	0	0.935475	6.408095e-02	0	0	0	22	0	5	326
OR10G7	390265	broad.mit.edu	37	11	123909404	123909404	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr11:123909404A>G	ENST00000330487.5	-	1	313	c.305T>C	c.(304-306)tTt>tCt	p.F102S		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GAAGTGGAAAAAATAGAGCTG	0.532																																						ENST00000330487.5	0.440000	2.700000e-01	0.400000	0.300000	0.340000	0.356037	0.340000	0.350000																										0				47						c.(304-306)tTt>tCt		olfactory receptor, family 10, subfamily G, member 7							124.0	133.0	130.0					11																	123909404		2200	4299	6499	SO:0001583	missense	390265	0	0					g.chr11:123909404A>G	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.305T>C	chr11.hg19:g.123909404A>G	ENSP00000329689:p.Phe102Ser	0						p.F102S	NM_001004463.1	NP_001004463.1	1	2	3	2.138887	Q8NGN6	O10G7_HUMAN		1	313	-		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	1	1	hg19	c.305T>C	CCDS31705.1	0	.	.	.	.	.	.	.	.	.	.	A	0.908	-0.719988	0.03182	.	.	ENSG00000182634	ENST00000330487	T	0.00502	6.95	3.39	-2.56	0.06268	3.39	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	1.214850	0.05929	N	0.634898	T	0.00524	0.0017	M	0.64630	1.985	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39165	-0.9627	10	0.41790	T	0.15	.	5.7826	0.18314	0.3487:0.4967:0.1546:0.0	.	102	Q8NGN6	O10G7_HUMAN	S	102	ENSP00000329689:F102S	ENSP00000329689:F102S	F	-	2	0	0	OR10G7	123414614	123414614	0.000000	0.05858	0.311000	0.25182	0.042000	0.13812	0.173000	0.16724	-0.386000	0.07821	-0.666000	0.03841	TTT	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.532	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	1	0	1	2	2	2	2	0	0	0	0	327	327	327	374	1	1.800000	-20.000000	1	0.560000	NM_001004463		0	63	57	0	578	508	0		1			0	0	327	0	0	1.000000	0	0	0	0	0	0	63	578
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	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.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	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	8.800000e-01	1.000000	0.980000	0.990000	0.989790	0.990000	1.000000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	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)	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	25349						c.(34-36)gGt>gAt		Kirsten rat sarcoma viral oncogene homolog							91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	2	121404	44	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.chr12:25398284C>T	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.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	1	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	p.G12D	NM_033360.2	NP_203524.1	2	2	4	2.495063	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	98	-	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.35G>A	CCDS8703.1	1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	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	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	0	KRAS	25289551	25289551	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	0.626866		TCGA-IB-AAUN-01A-12D-A38G-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	2	0	0	0	0	119	119	119	117	1	1.800000	-20.000000	1	0.560000	NM_033360		2229	76	75	5800	221	217	1	1	1	1	1	0	0	119	303	1	1.000000	9.884392e-01	1	9	116	14	335	76	221
BCL7A	605	broad.mit.edu	37	12	122492809	122492809	+	Missense_Mutation	SNP	G	G	A	rs148056282		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr12:122492809G>A	ENST00000261822.4	+	5	744	c.538G>A	c.(538-540)Gca>Aca	p.A180T	BCL7A_ENST00000538010.1_Missense_Mutation_p.A180T	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	180					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		GGGTCTGGCCGCAGAGACGTC	0.567			T	MYC	BNHL						OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(17;197 467 16477 23242 44349)	ENST00000261822.4	0.110000	1.000000e-02	0.080000	0.030000	0.050000	0.061866	0.050000	0.050000				Dom	yes			Dom	yes		12	12q24.1	12q24.1	605	T	B-cell CLL/lymphoma 7A				L	L	MYC		BNHL		0				18						c.(538-540)Gca>Aca		B-cell CLL/lymphoma 7A		G	THR/ALA,THR/ALA	0,4406		0,0,2203	70.0	77.0	74.0		538,538	0.1	0.0	12	dbSNP_134	74	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BCL7A	NM_001024808.1,NM_020993.3	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	180/211,180/232	122492809	1,13005	2203	4300	6503	SO:0001583	missense	605	4	121412	39				g.chr12:122492809G>A	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.538G>A	chr12.hg19:g.122492809G>A	ENSP00000261822:p.Ala180Thr	1		OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1519	BCL7A_ENST00000538010.1_Missense_Mutation_p.A180T	p.A180T	NM_001024808.1	NP_001019979.1	0	1	1	1.768437	Q4VC05	BCL7A_HUMAN		5	744	+	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	0	1	hg19	c.538G>A	CCDS53841.1	0	.	.	.	.	.	.	.	.	.	.	G	0.318	-0.963497	0.02249	0.0	1.16E-4	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.44083	0.93;1.01	6.07	0.0514	0.14297	6.07	0.0514	0.14297	.	0.533452	0.21468	N	0.074043	T	0.12774	0.0310	N	0.02539	-0.55	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.08055	0.003;0.002	T	0.28299	-1.0048	10	0.08837	T	0.75	.	5.2306	0.15420	0.4794:0.0:0.3844:0.1362	.	180;180	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	T	180	ENSP00000445868:A180T;ENSP00000261822:A180T	ENSP00000261822:A180T	A	+	1	0	0	BCL7A	120977192	120977192	0.318000	0.24598	0.000000	0.03702	0.001000	0.01503	0.660000	0.25009	-0.097000	0.12307	-0.137000	0.14449	GCA	0.413958		TCGA-IB-AAUN-01A-12D-A38G-08	0.567	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1	0	0	1	2	2	2	2	0	0	0	0	194	194	194	193	1	1.800000	-2.695311	1	0.560000			0	6	6	0	294	290	0		1	0		0	0	194	0	0	0.963916	4.996645e-02	0	0	0	15	0	6	294
CCNA1	8900	broad.mit.edu	37	13	37012789	37012789	+	Silent	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr13:37012789C>T	ENST00000255465.4	+	5	942	c.678C>T	c.(676-678)caC>caT	p.H226H	CCNA1_ENST00000440264.1_Silent_p.H182H|CCNA1_ENST00000418263.1_Silent_p.H225H|CCNA1_ENST00000449823.1_Silent_p.H182H			P78396	CCNA1_HUMAN	cyclin A1	226					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		AGATAAGGCACAGACCCAAAG	0.418																																						ENST00000255465.4	1.000000	7.400000e-01	1.000000	0.850000	0.980000	0.945373	0.980000	1.000000																										0				35						c.(676-678)caC>caT		cyclin A1							88.0	78.0	82.0					13																	37012789		2203	4300	6503	SO:0001819	synonymous_variant	8900	0	0					g.chr13:37012789C>T	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.678C>T	chr13.hg19:g.37012789C>T		0					CCNA1_ENST00000440264.1_Silent_p.H182H|CCNA1_ENST00000449823.1_Silent_p.H182H|CCNA1_ENST00000418263.1_Silent_p.H225H	p.H226H			0	0	0	2.116285	P78396	CCNA1_HUMAN	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	5	942	+		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Silent	SNP	ENST00000255465.4	1	1	hg19	c.678C>T	CCDS9357.1	1																																																																																								0.560000		TCGA-IB-AAUN-01A-12D-A38G-08	0.418	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	1	0	1	2	2	2	2	0	0	0	0	74	74	74	74	1	1.800000	-20.000000	1	0.560000	NM_003914		0	41	40	0	107	106	0		1			0	0	74	0	0	1.000000	0	0	0	0	0	0	41	107
KIAA0586	9786	broad.mit.edu	37	14	58915077	58915077	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr14:58915077C>T	ENST00000556134.1	+	8	1056	c.782C>T	c.(781-783)gCa>gTa	p.A261V	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_Missense_Mutation_p.A329V|KIAA0586_ENST00000423743.3_Missense_Mutation_p.A232V|KIAA0586_ENST00000261244.5_Missense_Mutation_p.A276V	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	261					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ATTAGTGCTGCACTCAAGACT	0.328																																						ENST00000556134.1	1.000000	8.000000e-01	0.990000	0.870000	0.940000	0.936437	0.940000	0.990000																										0				34						c.(781-783)gCa>gTa		KIAA0586							91.0	84.0	86.0					14																	58915077		1813	4077	5890	SO:0001583	missense	9786	0	0					g.chr14:58915077C>T	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.782C>T	chr14.hg19:g.58915077C>T	ENSP00000452351:p.Ala261Val	1					KIAA0586_ENST00000261244.5_Missense_Mutation_p.A276V|KIAA0586_ENST00000354386.6_Missense_Mutation_p.A329V|KIAA0586_ENST00000423743.3_Missense_Mutation_p.A232V|KIAA0586_ENST00000538571.2_3'UTR	p.A261V	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	0	1	1	1.546377	Q9BVV6	TALD3_HUMAN		8	1056	+			B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	1	1	hg19	c.782C>T	CCDS58321.1	1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801789	0.90538	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000555833;ENST00000261244;ENST00000546216	T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13	5.41	5.41	0.78517	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.75102	0.3804	M	0.68952	2.095	0.45239	D	0.998243	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.998;0.998;0.994;0.998;0.998	T	0.77038	-0.2736	10	0.87932	D	0	.	17.3225	0.87239	0.0:1.0:0.0:0.0	.	136;136;329;276;261;232	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	V	329;261;232;191;276;136	ENSP00000346359:A329V;ENSP00000452351:A261V;ENSP00000399427:A232V;ENSP00000450855:A191V;ENSP00000261244:A276V	ENSP00000261244:A276V	A	+	2	0	0	KIAA0586	57984830	57984830	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	4.520000	0.60524	2.696000	0.92011	0.585000	0.79938	GCA	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.328	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	1	0	1	2	2	2	2	0	0	0	0	115	115	115	115	1	1.800000	-20.000000	1	0.560000	NM_014749		0	70	69	0	105	104	1		1	0		0	0	115	0	0	1.000000	0	0	0	0	1	0	70	105
MYO5C	55930	broad.mit.edu	37	15	52536564	52536564	+	Silent	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr15:52536564C>T	ENST00000261839.7	-	19	2540	c.2379G>A	c.(2377-2379)caG>caA	p.Q793Q	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	793	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TCACAGTTTGCTGACCCCGGA	0.527																																						ENST00000261839.7	0.110000	1.000000e-02	0.080000	0.020000	0.040000	0.056967	0.040000	0.050000																										0				66						c.(2377-2379)caG>caA		myosin VC							62.0	69.0	67.0					15																	52536564		2134	4235	6369	SO:0001819	synonymous_variant	55930	0	0					g.chr15:52536564C>T	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2379G>A	chr15.hg19:g.52536564C>T		0					MYO5C_ENST00000443683.2_3'UTR	p.Q793Q	NM_018728.3	NP_061198.2	1	2	3	2.134988	Q9NQX4	MYO5C_HUMAN		19	2540	-			Q6P1W8	Silent	SNP	ENST00000261839.7	0	1	hg19	c.2379G>A	CCDS42036.1	0																																																																																								0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.527	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	0	0	1	2	2	2	2	0	0	0	0	123	123	123	122	1	1.800000	-2.808618	1	0.560000	NM_018728		0	5	5	0	369	363	0		1	0		0	0	123	0	0	0.934810	1.123582e-01	0	0	0	35	0	5	369
RAB27A	5873	broad.mit.edu	37	15	55497880	55497880	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr15:55497880G>A	ENST00000396307.2	-	6	742	c.491C>T	c.(490-492)gCt>gTt	p.A164V	RAB27A_ENST00000564609.1_Missense_Mutation_p.A164V|RAB27A_ENST00000336787.1_Missense_Mutation_p.A164V|RAB27A_ENST00000569493.1_Missense_Mutation_p.A164V	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	164					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CCCATTGGCAGCACTAGTTTC	0.443																																						ENST00000396307.2	0.120000	1.000000e-02	0.080000	0.020000	0.050000	0.058695	0.050000	0.050000																										0				9						c.(490-492)gCt>gTt		RAB27A, member RAS oncogene family							200.0	162.0	175.0					15																	55497880		2193	4292	6485	SO:0001583	missense	5873	0	0					g.chr15:55497880G>A	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"""RAB, member RAS oncogene"""	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.491C>T	chr15.hg19:g.55497880G>A	ENSP00000379601:p.Ala164Val	0					RAB27A_ENST00000569493.1_Missense_Mutation_p.A164V|RAB27A_ENST00000336787.1_Missense_Mutation_p.A164V|RAB27A_ENST00000564609.1_Missense_Mutation_p.A164V	p.A164V	NM_004580.4	NP_004571.2	1	2	3	2.134988	P51159	RB27A_HUMAN		6	742	-			O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	0	1	hg19	c.491C>T	CCDS10153.1	0	.	.	.	.	.	.	.	.	.	.	G	35	5.584941	0.96578	.	.	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	D;D	0.88818	-2.43;-2.43	5.49	5.49	0.81192	5.49	5.49	0.81192	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95494	0.8536	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96017	0.9006	10	0.87932	D	0	-18.6991	18.3593	0.90370	0.0:0.0:1.0:0.0	.	164	P51159	RB27A_HUMAN	V	164;156;164	ENSP00000379601:A164V;ENSP00000337761:A164V	ENSP00000337761:A164V	A	-	2	0	0	RAB27A	53285172	53285172	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.751000	0.98889	2.585000	0.87301	0.655000	0.94253	GCT	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.443	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	0	0	1	2	2	2	2	0	0	0	0	151	151	151	149	1	1.800000	-3.138838	1	0.560000	NM_004580, NM_183236		0	5	5	0	358	352	0		1	0		0	0	151	0	0	0.935186	2.308849e-01	0	0	0	55	0	5	358
BANP	54971	broad.mit.edu	37	16	88061097	88061097	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr16:88061097T>C	ENST00000393207.1	+	8	1101	c.880T>C	c.(880-882)Ttc>Ctc	p.F294L	BANP_ENST00000393208.2_Missense_Mutation_p.F263L|BANP_ENST00000355163.5_Missense_Mutation_p.F269L|BANP_ENST00000479780.2_Missense_Mutation_p.F263L|BANP_ENST00000355022.4_Missense_Mutation_p.F263L|BANP_ENST00000286122.7_Missense_Mutation_p.F294L|BANP_ENST00000538234.1_Missense_Mutation_p.F302L	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	294	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.|Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		AGGTCACCTTTTCTATAAATT	0.617																																						ENST00000393207.1	1.000000	8.800000e-01	1.000000	0.970000	0.990000	0.987920	0.990000	1.000000																										0				12						c.(880-882)Ttc>Ctc		BTG3 associated nuclear protein							64.0	67.0	66.0					16																	88061097		2198	4300	6498	SO:0001583	missense	54971	0	0					g.chr16:88061097T>C	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.880T>C	chr16.hg19:g.88061097T>C	ENSP00000376902:p.Phe294Leu	0					BANP_ENST00000393208.2_Missense_Mutation_p.F263L|BANP_ENST00000355163.5_Missense_Mutation_p.F269L|BANP_ENST00000479780.2_Missense_Mutation_p.F263L|BANP_ENST00000355022.4_Missense_Mutation_p.F263L|BANP_ENST00000538234.1_Missense_Mutation_p.F302L|BANP_ENST00000286122.7_Missense_Mutation_p.F294L	p.F294L	NM_001173543.1	NP_001167014.1	1	2	3	2.131575	Q8N9N5	BANP_HUMAN		8	1101	+			A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	1	1	hg19	c.880T>C	CCDS54054.1	1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049507	0.75846	.	.	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.5	5.5	0.81552	5.5	5.5	0.81552	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.34106	0.0886	N	0.14661	0.345	0.58432	D	0.999999	P;D;D;D;P;D	0.65815	0.951;0.973;0.963;0.995;0.954;0.993	P;P;D;D;D;D	0.77557	0.696;0.872;0.966;0.989;0.916;0.99	T	0.26538	-1.0100	10	0.51188	T	0.08	-0.7334	14.7894	0.69827	0.0:0.0:0.0:1.0	.	302;269;263;294;263;263	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	L	294;269;259;263;263;263;263;302;294	ENSP00000286122:F294L;ENSP00000347290:F269L;ENSP00000432508:F263L;ENSP00000376903:F263L;ENSP00000347125:F263L;ENSP00000444352:F302L;ENSP00000376902:F294L	ENSP00000286122:F294L	F	+	1	0	0	BANP	86618598	86618598	1.000000	0.71417	0.923000	0.36655	0.252000	0.25951	7.305000	0.78891	2.090000	0.63153	0.379000	0.24179	TTC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.617	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	1	0	1	2	2	2	2	0	0	0	0	141	141	141	140	1	1.800000	-20.000000	1	0.560000	NM_017869		0	94	92	0	222	216	1		1	1		0	0	141	0	0	1.000000	9.833710e-01	0	3	0	15	0	94	222
MYH2	4620	broad.mit.edu	37	17	10436865	10436865	+	Silent	SNP	G	G	A	rs146411264		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr17:10436865G>A	ENST00000245503.5	-	20	2649	c.2265C>T	c.(2263-2265)atC>atT	p.I755I	RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Silent_p.I755I|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	755	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GGTCAATGTCGATGGATGCAA	0.403																																						ENST00000245503.5	0.070000	1.000000e-02	0.060000	0.020000	0.030000	0.042978	0.030000	0.040000																										0				176						c.(2263-2265)atC>atT		myosin, heavy chain 2, skeletal muscle, adult		G	,	0,4406		0,0,2203	156.0	146.0	149.0		2265,2265	-8.1	0.7	17	dbSNP_134	149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	MYH2	NM_001100112.1,NM_017534.5	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	755/1942,755/1942	10436865	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4620	5	121412	43				g.chr17:10436865G>A		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.2265C>T	chr17.hg19:g.10436865G>A		1					RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000397183.2_Silent_p.I755I|CTC-297N7.11_ENST00000587182.2_RNA	p.I755I	NM_017534.5	NP_060004.3	0	1	1	1.564307	Q9UKX2	MYH2_HUMAN		20	2649	-			A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	0	1	hg19	c.2265C>T	CCDS11156.1	0																																																																																								0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.403	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	0	0	1	2	8	2	2	1	1	1	1	286	286	286	285	1	1.800000	-2.425391	0	0.560000	NM_017534		0	7	7	0	468	463	0		0			1	0	286	0	0	0.488302	0	0	0	0	0	0	7	468
TP53	7157	broad.mit.edu	37	17	7574018	7574018	+	Missense_Mutation	SNP	G	G	A	rs587782529		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr17:7574018G>A	ENST00000269305.4	-	10	1198	c.1009C>T	c.(1009-1011)Cgc>Tgc	p.R337C	TP53_ENST00000359597.4_Intron|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.R337C	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	337	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9452042}.|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11481490}.|R -> L (in sporadic cancers; somatic mutation).|R -> P (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.R337C(18)|p.0?(8)|p.R337fs*8(2)|p.R337G(1)|p.?(1)|p.I332fs*5(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)	ATCTCGAAGCGCTCACGCCCA	0.522		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	7.800000e-01	0.990000	0.870000	0.940000	0.932967	0.940000	0.990000		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		31	Substitution - Missense(19)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(1)	p.R337C(18)|p.0?(8)|p.R337fs*8(2)|p.R337G(1)|p.?(1)|p.I332fs*5(1)	central_nervous_system(6)|large_intestine(5)|ovary(4)|bone(4)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|stomach(1)|liver(1)|peritoneum(1)|lung(1)|kidney(1)	24185	GRCh37	CM981929	TP53	M		c.(1009-1011)Cgc>Tgc	Other conserved DNA damage response genes	tumor protein p53	Acetylsalicylic acid(DB00945)						56.0	44.0	48.0					17																	7574018		2203	4300	6503	SO:0001583	missense	7157	1	121410	29	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.chr17:7574018G>A	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.1009C>T	chr17.hg19:g.7574018G>A	ENSP00000269305:p.Arg337Cys	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.R337C|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000359597.4_Intron|TP53_ENST00000413465.2_Intron	p.R337C	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	1.564307	P04637	P53_HUMAN		10	1198	-		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.1009C>T	CCDS11118.1	1	.	.	.	.	.	.	.	.	.	.	G	9.719	1.159246	0.21454	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.95205	-3.64;-3.64	5.43	3.38	0.38709	5.43	3.38	0.38709	p53, tetramerisation domain (3);	0.000000	0.85682	D	0.000000	D	0.94321	0.8175	M	0.82323	2.585	0.48341	D	0.999635	P	0.39940	0.696	B	0.40940	0.344	D	0.93083	0.6493	10	0.87932	D	0	-7.3279	12.447	0.55657	0.0:0.0:0.6947:0.3053	.	337	P04637	P53_HUMAN	C	337;337;326	ENSP00000269305:R337C;ENSP00000391478:R337C	ENSP00000269305:R337C	R	-	1	0	0	TP53	7514743	7514743	0.558000	0.26554	0.006000	0.13384	0.274000	0.26718	1.012000	0.29924	0.615000	0.30124	0.561000	0.74099	CGC	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	2	2	2	2	0	0	0	0	50	50	50	50	1	1.800000	-20.000000	1	0.560000	NM_000546		0	38	37	0	48	45	1		1	1	1	0	0	50	550	0	1.000000	1	1	30	271	24	412	38	48
DBF4B	80174	broad.mit.edu	37	17	42828492	42828492	+	Silent	SNP	G	G	A	rs148114647	byFrequency	TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr17:42828492G>A	ENST00000315005.3	+	14	1857	c.1719G>A	c.(1717-1719)ccG>ccA	p.P573P	DBF4B_ENST00000393547.2_Intron	NM_145663.2	NP_663696.1	Q8NFT6	DBF4B_HUMAN	DBF4 zinc finger B	573					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of protein kinase activity (GO:0045860)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)	7		Prostate(33;0.0322)				CCTCACATCCGTGTACCCTTG	0.547																																						ENST00000315005.3	1.000000	5.600000e-01	0.760000	0.610000	0.680000	0.698179	0.680000	0.680000																										0				7						c.(1717-1719)ccG>ccA		DBF4 zinc finger B		G	,	2,4404	4.2+/-10.8	0,2,2201	126.0	106.0	113.0		,1719	-4.8	0.0	17	dbSNP_134	113	5,8595	4.3+/-15.6	0,5,4295	no	intron,coding-synonymous	DBF4B	NM_025104.3,NM_145663.2	,	0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538	,	,573/616	42828492	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	80174	14	121412	47				g.chr17:42828492G>A	AF465820	CCDS11485.1, CCDS45706.1, CCDS45706.2	17q21.31	2014-02-17	2014-02-17		ENSG00000161692	ENSG00000161692		"""Zinc fingers, DBF-type"""	17883	protein-coding gene	gene with protein product	"""chiffon homolog B (Drosophila)"", ""zinc finger, DBF-type containing 1B"""	611661	"""DBF4 homolog B (S. cerevisiae)"""			15668232	Standard	NM_145663		Approved	FLJ13087, DRF1, ASKL1, chifb, ZDBF1B	uc002ihf.3	Q8NFT6	OTTHUMG00000165717	ENST00000315005.3:c.1719G>A	chr17.hg19:g.42828492G>A		0					DBF4B_ENST00000393547.2_Intron	p.P573P	NM_145663.2	NP_663696.1	1	2	3	2.182111	Q8NFT6	DBF4B_HUMAN		14	1857	+		Prostate(33;0.0322)	D3DX56|Q8TEX0|Q96B19|Q9H912	Silent	SNP	ENST00000315005.3	1	1	hg19	c.1719G>A	CCDS11485.1	0																																																																																								0.567270		TCGA-IB-AAUN-01A-12D-A38G-08	0.547	DBF4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385930.1	1	0	1	2	2	2	2	0	0	0	0	239	239	239	234	1	1.800000	-3.439637	1	0.560000	NM_025104		0	100	99	0	434	421	1		1	0		0	0	239	0	0	1.000000	3.579171e-02	0	1	0	1	0	100	434
LRRC30	339291	broad.mit.edu	37	18	7231664	7231664	+	Silent	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr18:7231664G>A	ENST00000383467.2	+	1	542	c.528G>A	c.(526-528)gcG>gcA	p.A176A		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	176								p.A176A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						ACTTCTTCGCGCACATCCCCA	0.552																																						ENST00000383467.2	1.000000	0	0.080000	0.020000	0.040000	0.095817	0.040000	0.040000																										1	Substitution - coding silent(1)	p.A176A(1)	large_intestine(1)	31						c.(526-528)gcG>gcA		leucine rich repeat containing 30							96.0	103.0	100.0					18																	7231664		2112	4226	6338	SO:0001819	synonymous_variant	339291	2	121082	31				g.chr18:7231664G>A		CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422			30219	protein-coding gene	gene with protein product							Standard	NM_001105581		Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.528G>A	chr18.hg19:g.7231664G>A		0						p.A176A	NM_001105581.1	NP_001099051.1	1	2	3	2.180031	A6NM36	LRC30_HUMAN		1	542	+				Silent	SNP	ENST00000383467.2	0	1	hg19	c.528G>A	CCDS42409.1	0																																																																																								0.567270		TCGA-IB-AAUN-01A-12D-A38G-08	0.552	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442140.1	0	0	1	2	10	2	2	1	1	1	1	195	195	195	193	1	1.800000	-2.239799	0	0.560000	XM_292678		0	5	5	0	416	409	0		0			1	0	195	0	0	0.139044	0	0	0	0	0	0	5	416
TCF4	6925	broad.mit.edu	37	18	52899813	52899813	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr18:52899813T>C	ENST00000356073.4	-	17	2187	c.1576A>G	c.(1576-1578)Acg>Gcg	p.T526A	TCF4_ENST00000398339.1_Missense_Mutation_p.T628A|TCF4_ENST00000564403.2_Missense_Mutation_p.T532A|TCF4_ENST00000561831.3_Missense_Mutation_p.T366A|TCF4_ENST00000537856.3_Missense_Mutation_p.T396A|TCF4_ENST00000561992.1_Missense_Mutation_p.T396A|TCF4_ENST00000567880.1_Missense_Mutation_p.T466A|TCF4_ENST00000566279.1_Missense_Mutation_p.T466A|TCF4_ENST00000564999.1_Missense_Mutation_p.T526A|TCF4_ENST00000564228.1_Missense_Mutation_p.T455A|TCF4_ENST00000540999.1_Missense_Mutation_p.T502A|TCF4_ENST00000570177.2_Missense_Mutation_p.T396A|TCF4_ENST00000570287.2_Missense_Mutation_p.T366A|TCF4_ENST00000354452.3_Missense_Mutation_p.T526A|TCF4_ENST00000568673.1_Missense_Mutation_p.T502A|TCF4_ENST00000544241.2_Missense_Mutation_p.T455A|TCF4_ENST00000537578.1_Missense_Mutation_p.T502A|TCF4_ENST00000543082.1_Missense_Mutation_p.T484A|TCF4_ENST00000457482.3_Missense_Mutation_p.T366A|TCF4_ENST00000565018.2_Missense_Mutation_p.T526A|TCF4_ENST00000566286.1_Missense_Mutation_p.T523A|TCF4_ENST00000568740.1_Missense_Mutation_p.T501A	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	526					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GAAGATTTCGTGTCTTGCAGG	0.453																																						ENST00000356073.4	1.000000	8.900000e-01	1.000000	0.930000	0.970000	0.970826	0.970000	0.990000																										0				41						c.(1576-1578)Acg>Gcg		transcription factor 4							147.0	121.0	130.0					18																	52899813		2203	4300	6503	SO:0001583	missense	6925	0	0					g.chr18:52899813T>C	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1576A>G	chr18.hg19:g.52899813T>C	ENSP00000348374:p.Thr526Ala	1					TCF4_ENST00000398339.1_Missense_Mutation_p.T628A|TCF4_ENST00000564999.1_Missense_Mutation_p.T526A|TCF4_ENST00000564403.2_Missense_Mutation_p.T532A|TCF4_ENST00000567880.1_Missense_Mutation_p.T466A|TCF4_ENST00000568740.1_Missense_Mutation_p.T501A|TCF4_ENST00000561831.3_Missense_Mutation_p.T366A|TCF4_ENST00000566286.1_Missense_Mutation_p.T523A|TCF4_ENST00000561992.1_Missense_Mutation_p.T396A|TCF4_ENST00000537578.1_Missense_Mutation_p.T502A|TCF4_ENST00000570287.2_Missense_Mutation_p.T366A|TCF4_ENST00000565018.2_Missense_Mutation_p.T526A|TCF4_ENST00000540999.1_Missense_Mutation_p.T502A|TCF4_ENST00000570177.2_Missense_Mutation_p.T396A|TCF4_ENST00000457482.3_Missense_Mutation_p.T366A|TCF4_ENST00000543082.1_Missense_Mutation_p.T484A|TCF4_ENST00000537856.3_Missense_Mutation_p.T396A|TCF4_ENST00000568673.1_Missense_Mutation_p.T502A|TCF4_ENST00000544241.2_Missense_Mutation_p.T455A|TCF4_ENST00000564228.1_Missense_Mutation_p.T455A|TCF4_ENST00000566279.1_Missense_Mutation_p.T466A|TCF4_ENST00000354452.3_Missense_Mutation_p.T526A	p.T526A	NM_003199.2	NP_003190.1	0	1	1	1.553807	P15884	ITF2_HUMAN		17	2187	-			B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	1	1	hg19	c.1576A>G	CCDS11960.1	1	.	.	.	.	.	.	.	.	.	.	T	2.304	-0.359529	0.05138	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.16897	2.57;2.31;2.62;2.62;2.62;2.57;2.56;2.37;2.55	5.35	4.18	0.49190	5.35	4.18	0.49190	.	0.176553	0.51477	D	0.000093	T	0.05777	0.0151	N	0.03050	-0.425	0.38345	D	0.944171	B;B;B;B;B;B;B;B;B	0.18310	0.0;0.016;0.001;0.027;0.0;0.0;0.001;0.0;0.01	B;B;B;B;B;B;B;B;B	0.23150	0.001;0.015;0.001;0.044;0.0;0.001;0.002;0.0;0.003	T	0.24977	-1.0145	10	0.09590	T	0.72	-5.2262	5.6177	0.17440	0.1509:0.0821:0.0:0.767	.	502;526;366;628;526;484;455;366;523	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	A	526;366;526;484;502;502;455;396;628	ENSP00000346440:T526A;ENSP00000409447:T366A;ENSP00000348374:T526A;ENSP00000439656:T484A;ENSP00000445202:T502A;ENSP00000440731:T502A;ENSP00000441562:T455A;ENSP00000439827:T396A;ENSP00000381382:T628A	ENSP00000346440:T526A	T	-	1	0	0	TCF4	51050811	51050811	0.997000	0.39634	1.000000	0.80357	0.979000	0.70002	0.581000	0.23819	0.872000	0.35775	0.383000	0.25322	ACG	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.453	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	1	0	1	2	2	2	2	0	0	0	0	151	151	151	150	1	1.800000	-20.000000	1	0.560000	NM_003199		0	115	114	0	148	145	1		1	1		0	0	151	0	0	1.000000	1	0	2	0	49	0	115	148
ACPT	93650	broad.mit.edu	37	19	51298323	51298323	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr19:51298323G>A	ENST00000270593.1	+	11	1189	c.1189G>A	c.(1189-1191)Gga>Aga	p.G397R	ACPT_ENST00000270594.3_Missense_Mutation_p.G304R|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	397						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CCTGCTGGCCGGAGCTGTAGC	0.677																																						ENST00000270593.1	1.000000	4.700000e-01	1.000000	0.650000	0.870000	0.843443	0.870000	1.000000																										0				11						c.(1189-1191)Gga>Aga		acid phosphatase, testicular							17.0	17.0	17.0					19																	51298323		2196	4289	6485	SO:0001583	missense	93650	1	120938	30				g.chr19:51298323G>A	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.1189G>A	chr19.hg19:g.51298323G>A	ENSP00000270593:p.Gly397Arg	0					CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Missense_Mutation_p.G304R	p.G397R	NM_033068.2	NP_149059.1	1	2	3	2.162368	Q9BZG2	PPAT_HUMAN		11	1189	+		all_neural(266;0.057)	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	0	1	hg19	c.1189G>A	CCDS12802.1	1	.	.	.	.	.	.	.	.	.	.	g	18.35	3.605092	0.66445	.	.	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.13420	2.76;2.59	4.14	4.14	0.48551	4.14	4.14	0.48551	.	0.282362	0.27117	N	0.020860	T	0.24198	0.0586	L	0.41824	1.3	0.33730	D	0.618158	D	0.89917	1.0	D	0.68483	0.958	T	0.16660	-1.0395	10	0.25106	T	0.35	-8.8258	12.3028	0.54884	0.0:0.0:1.0:0.0	.	397	Q9BZG2	PPAT_HUMAN	R	397;304	ENSP00000270593:G397R;ENSP00000270594:G304R	ENSP00000270593:G397R	G	+	1	0	0	ACPT	55990135	55990135	0.999000	0.42202	0.983000	0.44433	0.808000	0.45660	4.443000	0.59994	2.037000	0.60232	0.561000	0.74099	GGA	0.564873		TCGA-IB-AAUN-01A-12D-A38G-08	0.677	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	0	0	1	2	2	2	2	0	0	0	0	23	23	23	23	1	1.800000	-19.904370	1	0.560000	NM_033068		0	10	7	0	32	32	0		1			0	0	23	0	0	0.997107	0	0	0	0	0	0	10	32
PEG3	5178	broad.mit.edu	37	19	57328906	57328906	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr19:57328906G>A	ENST00000326441.9	-	10	1267	c.904C>T	c.(904-906)Cgg>Tgg	p.R302W	ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.R178W|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R302W|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R176W	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	302					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CAAATCCCCCGCCGGTGGGTT	0.458																																						ENST00000326441.9	1.000000	7.900000e-01	1.000000	0.860000	0.940000	0.935868	0.940000	1.000000																										0				170						c.(904-906)Cgg>Tgg		paternally expressed 3							49.0	57.0	54.0					19																	57328906		2203	4299	6502	SO:0001583	missense	5178	2	121376	36				g.chr19:57328906G>A	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.904C>T	chr19.hg19:g.57328906G>A	ENSP00000326581:p.Arg302Trp	0					PEG3_ENST00000598410.1_Missense_Mutation_p.R178W|PEG3_ENST00000423103.2_Missense_Mutation_p.R302W|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R176W|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron	p.R302W	NM_006210.2	NP_006201.1	1	2	3	2.158275	Q9GZU2	PEG3_HUMAN		10	1267	-		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	1	1	hg19	c.904C>T	CCDS12948.1	1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475230	0.63737	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02737	4.18;4.18	4.27	3.22	0.36961	4.27	3.22	0.36961	.	0.000000	0.43919	D	0.000511	T	0.06962	0.0177	L	0.27053	0.805	.	.	.	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.73708	0.972;0.972;0.981	T	0.36407	-0.9749	9	0.51188	T	0.08	-23.6433	11.7512	0.51849	0.0:0.0:0.8225:0.1775	.	178;302;237	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	W	302;302;272	ENSP00000326581:R302W;ENSP00000403051:R302W	ENSP00000292074:R272W	R	-	1	2	2	ZIM2	62020718	62020718	0.147000	0.22687	0.499000	0.27577	0.991000	0.79684	3.450000	0.52957	1.367000	0.46095	0.561000	0.74099	CGG	0.564873		TCGA-IB-AAUN-01A-12D-A38G-08	0.458	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2	1	0	1	2	10	2	2	1	1	1	1	193	193	193	188	1	1.800000	-5.989526	1	0.560000			0	122	120	0	346	333	1		1			1	0	193	0	0	1.000000	0	0	0	0	0	0	122	346
ATXN7L2	127002	broad.mit.edu	37	1	110032901	110032901	+	Silent	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:110032901C>T	ENST00000369870.3	+	9	1260	c.1245C>T	c.(1243-1245)acC>acT	p.T415T		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	415										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGTTCTGCACCTTTGGGAGCC	0.597											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000369870.3	0.110000	1.000000e-02	0.080000	0.030000	0.050000	0.061723	0.050000	0.050000																										0				17						c.(1243-1245)acC>acT		ataxin 7-like 2							104.0	94.0	97.0					1																	110032901		2203	4300	6503	SO:0001819	synonymous_variant	127002	0	0					g.chr1:110032901C>T	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1245C>T	chr1.hg19:g.110032901C>T		1		OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1424		p.T415T	NM_153340.4	NP_699171.3	0	1	1	1.538419	Q5T6C5	AT7L2_HUMAN		9	1260	+		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Silent	SNP	ENST00000369870.3	0	1	hg19	c.1245C>T	CCDS30794.1	0																																																																																								0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.597	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	0	0	1	2	2	2	2	0	0	0	0	186	186	186	184	1	1.800000	-2.434781	0	0.560000	NM_153340		0	6	6	0	282	278	0		1	0		0	0	186	0	0	0.963877	6.635857e-04	0	0	0	2	0	6	282
MTOR	2475	broad.mit.edu	37	1	11217239	11217239	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:11217239C>T	ENST00000361445.4	-	30	4515	c.4439G>A	c.(4438-4440)cGc>cAc	p.R1480H		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1480	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GCAGCGCATGCGGCCCAGCAT	0.532																																						ENST00000361445.4	0.070000	0	0.050000	0.010000	0.020000	0.036310	0.020000	0.030000																										0				149						c.(4438-4440)cGc>cAc		mechanistic target of rapamycin (serine/threonine kinase)	Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)						192.0	176.0	181.0					1																	11217239		2203	4300	6503	SO:0001583	missense	2475	1	121412	33				g.chr1:11217239C>T	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4439G>A	chr1.hg19:g.11217239C>T	ENSP00000354558:p.Arg1480His	1						p.R1480H	NM_004958.3	NP_004949.1	0	1	1	1.591539	P42345	MTOR_HUMAN		30	4515	-			Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	0	1	hg19	c.4439G>A	CCDS127.1	0	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577708	0.65878	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.65549	-0.16	5.32	5.32	0.75619	5.32	5.32	0.75619	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53867	0.1823	L	0.31926	0.97	0.80722	D	1	B	0.13145	0.007	B	0.01281	0.0	T	0.46190	-0.9209	10	0.30854	T	0.27	-1.1882	19.0009	0.92834	0.0:1.0:0.0:0.0	.	1480	P42345	MTOR_HUMAN	H	1480	ENSP00000354558:R1480H	ENSP00000354558:R1480H	R	-	2	0	0	MTOR	11139826	11139826	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.414000	0.80117	2.486000	0.83907	0.655000	0.94253	CGC	0.391256		TCGA-IB-AAUN-01A-12D-A38G-08	0.532	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	0	0	1	2	2	2	2	0	0	0	0	260	260	260	259	1	1.800000	-1.773933	0	0.560000	NM_004958		0	5	5	0	418	409	0		1	0		0	0	260	0	0	0.934298	4.200110e-02	0	0	0	22	0	5	418
PLA2G2C	391013	broad.mit.edu	37	1	20501534	20501534	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:20501534C>A	ENST00000429261.2	-	2	205	c.145G>T	c.(145-147)Ggg>Tgg	p.G49W	PLA2G2C_ENST00000247992.5_Missense_Mutation_p.G52W|PLA2G2C_ENST00000495760.2_5'UTR			Q5R387	PA2GC_HUMAN	phospholipase A2, group IIC	49					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(1)	7		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.14e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.000528)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCTTTATCCCCAAGCCCACAG	0.502																																						ENST00000429261.2	0.210000	3.000000e-02	0.150000	0.060000	0.100000	0.112572	0.100000	0.100000																										0				7						c.(145-147)Ggg>Tgg		phospholipase A2, group IIC							57.0	63.0	61.0					1																	20501534		1964	4165	6129	SO:0001583	missense	391013	0	0					g.chr1:20501534C>A			1p36.12	2010-06-04	2003-10-13		ENSG00000187980	ENSG00000187980			9032	protein-coding gene	gene with protein product			"""phospholipase A2, group IIC (possible pseudogene)"""			8838795	Standard	NM_001105572		Approved		uc009vpq.1	Q5R387	OTTHUMG00000002705	ENST00000429261.2:c.145G>T	chr1.hg19:g.20501534C>A	ENSP00000389335:p.Gly49Trp	1					PLA2G2C_ENST00000495760.2_5'UTR|PLA2G2C_ENST00000247992.5_Missense_Mutation_p.G52W	p.G49W			0	1	1	1.605528	Q5R387	PA2GC_HUMAN		2	205	-		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)	Q7M4M6	Missense_Mutation	SNP	ENST00000429261.2	0	1	hg19	c.145G>T		0	.	.	.	.	.	.	.	.	.	.	C	18.49	3.635175	0.67130	.	.	ENSG00000187980	ENST00000429261;ENST00000247992	T;D	0.86030	1.34;-2.06	5.13	5.13	0.70059	5.13	5.13	0.70059	.	0.000000	0.56097	D	0.000031	D	0.94621	0.8266	H	0.96142	3.775	0.50632	D	0.99988	.	.	.	.	.	.	D	0.95955	0.8957	8	0.87932	D	0	.	14.0795	0.64912	0.0:1.0:0.0:0.0	.	.	.	.	W	49;52	ENSP00000389335:G49W;ENSP00000247992:G52W	ENSP00000247992:G52W	G	-	1	0	0	PLA2G2C	20374121	20374121	0.879000	0.30193	1.000000	0.80357	0.765000	0.43378	2.413000	0.44618	2.364000	0.80123	0.655000	0.94253	GGG	0.391256		TCGA-IB-AAUN-01A-12D-A38G-08	0.502	PLA2G2C-001	PUTATIVE	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000007689.3	0	0	1	2	2	2	2	0	0	0	0	115	115	115	115	1	1.800000	-3.426894	1	0.560000	NM_001105572		0	5	5	0	129	123	0		1			0	0	115	0	0	0.930963	0	0	0	0	0	0	5	129
AMPD2	271	broad.mit.edu	37	1	110172900	110172900	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:110172900G>A	ENST00000256578.3	+	16	2551	c.2191G>A	c.(2191-2193)Gcc>Acc	p.A731T	AMPD2_ENST00000342115.4_Missense_Mutation_p.A650T|AMPD2_ENST00000528667.1_Missense_Mutation_p.A731T|AMPD2_ENST00000526301.1_3'UTR|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000358729.4_Missense_Mutation_p.A656T|AMPD2_ENST00000528454.1_Missense_Mutation_p.A613T|AMPD2_ENST00000393688.3_Missense_Mutation_p.A612T	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	731					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		GATCGGCATCGCCATGTCTCC	0.652																																						ENST00000256578.3	0.080000	1.000000e-02	0.060000	0.020000	0.030000	0.045042	0.030000	0.040000																										0				7						c.(2191-2193)Gcc>Acc		adenosine monophosphate deaminase 2							143.0	144.0	144.0					1																	110172900		2203	4300	6503	SO:0001583	missense	271	0	0					g.chr1:110172900G>A	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"""AMPD isoform L"""	102771	"""adenosine monophosphate deaminase 2 (isoform L)"""			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.2191G>A	chr1.hg19:g.110172900G>A	ENSP00000256578:p.Ala731Thr	1					AMPD2_ENST00000393688.3_Missense_Mutation_p.A612T|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000528454.1_Missense_Mutation_p.A613T|AMPD2_ENST00000528667.1_Missense_Mutation_p.A731T|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Missense_Mutation_p.A656T|AMPD2_ENST00000342115.4_Missense_Mutation_p.A650T	p.A731T	NM_004037.7	NP_004028.3	0	1	1	1.538419	Q01433	AMPD2_HUMAN		16	2551	+		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	SNP	ENST00000256578.3	0	1	hg19	c.2191G>A	CCDS805.1	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.324955|5.324955	0.95708|0.95708	.|.	.|.	ENSG00000116337|ENSG00000116337	ENST00000342115;ENST00000528667;ENST00000256578;ENST00000358729;ENST00000528454;ENST00000393688|ENST00000369840	D;D;D;D;D;D|.	0.83335|.	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71|.	4.66|4.66	4.66|4.66	0.58398|0.58398	4.66|4.66	4.66|4.66	0.58398|0.58398	Adenosine/AMP deaminase (1);|.	0.102270|.	0.64402|.	D|.	0.000003|.	T|T	0.67344|0.67344	0.2883|0.2883	M|M	0.69358|0.69358	2.11|2.11	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;0.993;0.989;0.999|.	D;P;P;P|.	0.85130|.	0.997;0.739;0.705;0.873|.	T|T	0.66999|0.66999	-0.5781|-0.5781	10|5	0.54805|.	T|.	0.06|.	-24.088|-24.088	17.3347|17.3347	0.87277|0.87277	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	656;612;731;650|.	Q01433-4;Q01433-3;Q01433;Q01433-2|.	.;.;AMPD2_HUMAN;.|.	T|H	650;731;731;656;613;612|701	ENSP00000345498:A650T;ENSP00000436541:A731T;ENSP00000256578:A731T;ENSP00000351573:A656T;ENSP00000437164:A613T;ENSP00000377292:A612T|.	ENSP00000256578:A731T|.	A|R	+|+	1|2	0|0	0|0	AMPD2|AMPD2	109974423|109974423	109974423|109974423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.780000|0.780000	0.44128|0.44128	9.595000|9.595000	0.98260|0.98260	2.424000|2.424000	0.82194|0.82194	0.561000|0.561000	0.74099|0.74099	GCC|CGC	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.652	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1	0	0	1	2	2	2	2	1	1	1	0	303	303	303	302	1	1.800000	-2.420047	0	0.560000			0	6	6	0	390	379	0		1	0		1	0	303	0	0	0.962101	1.784174e-01	0	0	0	43	0	6	390
DTL	51514	broad.mit.edu	37	1	212209261	212209262	+	Missense_Mutation	DNP	CC	CC	GG			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:212209261_212209262CC>GG	ENST00000366991.4	+	1	343_344	c.29_30CC>GG	c.(28-30)cCC>cGG	p.P10R	INTS7_ENST00000366994.3_5'Flank|DTL_ENST00000542077.1_Missense_Mutation_p.P10R|INTS7_ENST00000366993.3_5'Flank|DTL_ENST00000475419.1_3'UTR|INTS7_ENST00000469606.1_5'Flank|INTS7_ENST00000366992.3_5'Flank|INTS7_ENST00000440600.2_5'Flank	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	10					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		CTCCGCCAGCCCCAGCTTGGCG	0.574																																						ENST00000366991.4	1.000000	7.300000e-01	1.000000	0.850000	0.980000	0.942114	0.980000	1.000000																										0				23						c.(28-30)cCc>cGc|c.(28-30)ccC>ccG		denticleless E3 ubiquitin protein ligase homolog (Drosophila)																																				SO:0001583	missense	51514	0	0					g.chr1:212209261C>G|g.chr1:212209262C>G	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	Exception_encountered	chr1.hg19:g.212209261_212209262delinsGG	ENSP00000355958:p.Pro10Arg	0					DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Missense_Mutation_p.P10R|INTS7_ENST00000366993.3_5'Flank|INTS7_ENST00000440600.2_5'Flank|INTS7_ENST00000366994.3_5'Flank|INTS7_ENST00000366992.3_5'Flank|INTS7_ENST00000469606.1_5'Flank|DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Silent_p.P10P|INTS7_ENST00000366993.3_5'Flank|INTS7_ENST00000440600.2_5'Flank|INTS7_ENST00000366994.3_5'Flank|INTS7_ENST00000366992.3_5'Flank|INTS7_ENST00000469606.1_5'Flank	p.P10R|p.P10P	NM_016448.2	NP_057532.2	1	2	3	2.136668	Q9NZJ0	DTL_HUMAN		1	343|344	+			A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Missense_Mutation|Silent	SNP	ENST00000366991.4	1	1	hg19	c.29C>G|c.30C>G	CCDS1502.1	1																									5.63|	5.63|	0.86233|																																												0|			210275884|														0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.574	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	1	0	1	2	2	2	2	0	0	0	0	76	78|76	78|76	78|76	1	1.800000	-20.000000|-4.772945	1	0.560000	NM_016448		0	38	38	0	100	96	1		1	1		0	0	78|76	0	0	1.000000	6.180417e-01	0	3	0	4	0	38	100
ESRRG	2104	broad.mit.edu	37	1	216680448	216680448	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:216680448C>A	ENST00000408911.3	-	7	1363	c.1210G>T	c.(1210-1212)Gct>Tct	p.A404S	ESRRG_ENST00000493603.1_Missense_Mutation_p.A381S|ESRRG_ENST00000493748.1_Missense_Mutation_p.A381S|ESRRG_ENST00000360012.3_Missense_Mutation_p.A381S|ESRRG_ENST00000361395.2_Missense_Mutation_p.A381S|ESRRG_ENST00000366938.2_Missense_Mutation_p.A381S|ESRRG_ENST00000361525.3_Missense_Mutation_p.A381S|ESRRG_ENST00000359162.2_Missense_Mutation_p.A381S|ESRRG_ENST00000463665.1_Missense_Mutation_p.A342S|ESRRG_ENST00000366940.2_Missense_Mutation_p.A381S|ESRRG_ENST00000391890.3_Missense_Mutation_p.A388S|ESRRG_ENST00000487276.1_Missense_Mutation_p.A381S|ESRRG_ENST00000366937.1_Missense_Mutation_p.A416S	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	404					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	TGCTGGCCAGCTTCATAATCC	0.498																																						ENST00000408911.3	0.130000	2.000000e-02	0.100000	0.040000	0.060000	0.071202	0.060000	0.060000																										0				49						c.(1210-1212)Gct>Tct		estrogen-related receptor gamma	Diethylstilbestrol(DB00255)						114.0	101.0	106.0					1																	216680448		2203	4300	6503	SO:0001583	missense	2104	0	0					g.chr1:216680448C>A	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.1210G>T	chr1.hg19:g.216680448C>A	ENSP00000386171:p.Ala404Ser	0					ESRRG_ENST00000463665.1_Missense_Mutation_p.A342S|ESRRG_ENST00000366938.2_Missense_Mutation_p.A381S|ESRRG_ENST00000361525.3_Missense_Mutation_p.A381S|ESRRG_ENST00000493603.1_Missense_Mutation_p.A381S|ESRRG_ENST00000487276.1_Missense_Mutation_p.A381S|ESRRG_ENST00000359162.2_Missense_Mutation_p.A381S|ESRRG_ENST00000391890.3_Missense_Mutation_p.A388S|ESRRG_ENST00000366937.1_Missense_Mutation_p.A416S|ESRRG_ENST00000361395.2_Missense_Mutation_p.A381S|ESRRG_ENST00000493748.1_Missense_Mutation_p.A381S|ESRRG_ENST00000360012.3_Missense_Mutation_p.A381S|ESRRG_ENST00000366940.2_Missense_Mutation_p.A381S	p.A404S	NM_001438.3	NP_001429.2	1	2	3	2.136668	P62508	ERR3_HUMAN		7	1363	-			A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	0	1	hg19	c.1210G>T	CCDS41468.1	0	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847181	0.32606	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748	D;D;D;D;D;D;D;D;D;D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01	5.61	5.61	0.85477	5.61	5.61	0.85477	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.047654	0.85682	D	0.000000	D	0.91633	0.7356	N	0.12569	0.235	0.80722	D	1	B;B;B	0.10296	0.0;0.002;0.003	B;B;B	0.15052	0.008;0.012;0.012	D	0.86965	0.2094	10	0.19590	T	0.45	.	19.652	0.95819	0.0:1.0:0.0:0.0	.	342;416;404	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	S	381;381;416;404;381;381;381;381;381;388;342;381;381;381	ENSP00000355225:A381S;ENSP00000355907:A381S;ENSP00000355904:A416S;ENSP00000386171:A404S;ENSP00000352077:A381S;ENSP00000354584:A381S;ENSP00000355905:A381S;ENSP00000353108:A381S;ENSP00000419594:A381S;ENSP00000375761:A388S;ENSP00000418629:A342S;ENSP00000419155:A381S;ENSP00000417374:A381S	ENSP00000346386:A381S	A	-	1	0	0	ESRRG	214747071	214747071	1.000000	0.71417	0.973000	0.42090	0.976000	0.68499	4.892000	0.63193	2.656000	0.90262	0.561000	0.74099	GCT	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.498	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	0	0	1	2	9	2	2	1	1	1	1	244	244	244	243	1	1.800000	-3.176432	1	0.560000	NM_206595		0	8	8	0	442	432	0		0	0		1	0	244	0	0	0.479260	4.376112e-04	0	0	0	2	0	8	442
CHML	1122	broad.mit.edu	37	1	241797637	241797637	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:241797637T>C	ENST00000366553.1	-	1	1595	c.1432A>G	c.(1432-1434)Ata>Gta	p.I478V	OPN3_ENST00000469376.1_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000366554.2_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	478					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GGAGGAACTATCAGAATGGAA	0.428																																						ENST00000366553.1	0.370000	1.800000e-01	0.320000	0.220000	0.260000	0.271717	0.260000	0.260000																										0				26						c.(1432-1434)Ata>Gta		choroideremia-like (Rab escort protein 2)							96.0	94.0	94.0					1																	241797637		2203	4299	6502	SO:0001583	missense	1122	0	0					g.chr1:241797637T>C	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1432A>G	chr1.hg19:g.241797637T>C	ENSP00000355511:p.Ile478Val	0					OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron	p.I478V	NM_001821.3	NP_001812.2	1	2	3	2.136668	P26374	RAE2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0125)	1	1595	-	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	1	1	hg19	c.1432A>G	CCDS31073.1	0	.	.	.	.	.	.	.	.	.	.	T	6.570	0.473395	0.12461	.	.	ENSG00000203668	ENST00000366553	D	0.82167	-1.58	5.08	0.907	0.19321	5.08	0.907	0.19321	.	0.297564	0.35013	N	0.003520	T	0.66954	0.2842	.	.	.	0.21147	N	0.999771	B	0.02656	0.0	B	0.09377	0.004	T	0.53236	-0.8467	9	0.42905	T	0.14	-1.3604	0.6338	0.00799	0.164:0.2371:0.1696:0.4293	.	478	P26374	RAE2_HUMAN	V	478	ENSP00000355511:I478V	ENSP00000355511:I478V	I	-	1	0	0	CHML	239864260	239864260	0.971000	0.33674	0.988000	0.46212	0.919000	0.55068	1.313000	0.33585	0.059000	0.16252	-0.313000	0.08912	ATA	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.428	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	1	0	1	2	2	2	2	0	0	0	0	210	210	210	210	1	1.800000	-20.000000	1	0.560000	NM_001821		0	31	30	0	388	382	0		1	0		0	0	210	0	0	1.000000	2.312893e-01	0	0	0	12	0	31	388
ADPRHL2	54936	broad.mit.edu	37	1	36557583	36557583	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:36557583G>A	ENST00000373178.4	+	4	619	c.589G>A	c.(589-591)Gct>Act	p.A197T		NM_017825.2	NP_060295.1	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	197						mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(ADP-ribose) glycohydrolase activity (GO:0004649)			cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|pancreas(1)	8		Myeloproliferative disorder(586;0.0393)				GCAGGCCCTGGCTGTGCACCT	0.627																																						ENST00000373178.4	0.140000	1.000000e-02	0.100000	0.030000	0.060000	0.072386	0.060000	0.060000																										0				8						c.(589-591)Gct>Act		ADP-ribosylhydrolase like 2							67.0	67.0	67.0					1																	36557583		2203	4300	6503	SO:0001583	missense	54936	0	0					g.chr1:36557583G>A	AJ427295	CCDS402.1	1p34.3	2008-02-05			ENSG00000116863	ENSG00000116863			21304	protein-coding gene	gene with protein product		610624				12070318, 16278211	Standard	NM_017825		Approved	ARH3, FLJ20446	uc001bzt.3	Q9NX46	OTTHUMG00000007628	ENST00000373178.4:c.589G>A	chr1.hg19:g.36557583G>A	ENSP00000362273:p.Ala197Thr	1						p.A197T	NM_017825.2	NP_060295.1	0	1	1	1.571110	Q9NX46	ARHL2_HUMAN		4	619	+		Myeloproliferative disorder(586;0.0393)	Q53G94|Q6IAB8|Q9BY47	Missense_Mutation	SNP	ENST00000373178.4	0	1	hg19	c.589G>A	CCDS402.1	0	.	.	.	.	.	.	.	.	.	.	G	36	5.663119	0.96745	.	.	ENSG00000116863	ENST00000373178;ENST00000540867;ENST00000543954	T	0.35421	1.31	5.48	5.48	0.80851	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.64929	0.2643	M	0.85710	2.77	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.64067	-0.6494	10	0.30854	T	0.27	-11.8061	19.3486	0.94374	0.0:0.0:1.0:0.0	.	197	Q9NX46	ARHL2_HUMAN	T	197;117;43	ENSP00000362273:A197T	ENSP00000362273:A197T	A	+	1	0	0	ADPRHL2	36330170	36330170	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.845000	0.99498	2.546000	0.85860	0.655000	0.94253	GCT	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.627	ADPRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020199.1	0	0	1	2	2	2	2	0	0	0	0	107	107	107	106	1	1.800000	-5.993319	1	0.560000	NM_017825		0	4	4	0	170	165	0		1	0		0	0	107	0	0	0.884336	4.330435e-01	0	0	0	54	0	4	170
LRRC7	57554	broad.mit.edu	37	1	70488845	70488845	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:70488845C>T	ENST00000035383.5	+	15	1498	c.1468C>T	c.(1468-1470)Cgt>Tgt	p.R490C	RP11-181B18.1_ENST00000414132.1_RNA|LRRC7_ENST00000415775.2_Intron|RP11-181B18.1_ENST00000425754.1_RNA|LRRC7_ENST00000310961.5_Missense_Mutation_p.R495C	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	490						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						AAGGGGCCAGCGTGGGATTAC	0.542																																						ENST00000035383.5	1.000000	8.000000e-01	0.990000	0.880000	0.940000	0.940533	0.940000	0.990000																										0				162						c.(1468-1470)Cgt>Tgt		leucine rich repeat containing 7							52.0	48.0	49.0					1																	70488845		2203	4300	6503	SO:0001583	missense	57554	0	0					g.chr1:70488845C>T		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.1468C>T	chr1.hg19:g.70488845C>T	ENSP00000035383:p.Arg490Cys	1					LRRC7_ENST00000310961.5_Missense_Mutation_p.R495C|RP11-181B18.1_ENST00000425754.1_RNA|RP11-181B18.1_ENST00000414132.1_RNA|LRRC7_ENST00000415775.2_Intron	p.R490C	NM_020794.2	NP_065845.1	0	1	1	1.571110	Q96NW7	LRRC7_HUMAN		15	1498	+			Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	1	1	hg19	c.1468C>T	CCDS645.1	1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925926	0.52759	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000370957	T;T	0.38077	1.16;1.24	5.86	5.86	0.93980	5.86	5.86	0.93980	.	0.257341	0.35495	N	0.003162	T	0.10981	0.0268	N	0.08118	0	0.80722	D	1	P	0.49358	0.923	B	0.35859	0.212	T	0.05273	-1.0895	10	0.72032	D	0.01	.	15.6849	0.77402	0.0:1.0:0.0:0.0	.	490	Q96NW7	LRRC7_HUMAN	C	495;490;313	ENSP00000309245:R495C;ENSP00000035383:R490C	ENSP00000035383:R490C	R	+	1	0	0	LRRC7	70261433	70261433	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.522000	0.53480	2.775000	0.95449	0.585000	0.79938	CGT	0.388889		TCGA-IB-AAUN-01A-12D-A38G-08	0.542	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	1	0	1	2	2	2	2	0	0	0	0	96	96	96	95	1	1.800000	-20.000000	1	0.560000	NM_020794		0	56	56	0	77	74	1		1			0	0	96	0	0	1.000000	0	0	0	0	0	0	56	77
OR2G2	81470	broad.mit.edu	37	1	247752184	247752184	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr1:247752184C>T	ENST00000320065.1	+	1	523	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R175C(1)		endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CTGTGGGCATCGCCAAGTGGA	0.557																																						ENST00000320065.1	0.110000	0	0.080000	0.020000	0.040000	0.053113	0.040000	0.040000																										1	Substitution - Missense(1)	p.R175C(1)	large_intestine(1)	45						c.(523-525)Cgc>Tgc		olfactory receptor, family 2, subfamily G, member 2							184.0	171.0	175.0					1																	247752184		2203	4300	6503	SO:0001583	missense	81470	0	0					g.chr1:247752184C>T	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.523C>T	chr1.hg19:g.247752184C>T	ENSP00000326349:p.Arg175Cys	0					RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	p.R175C	NM_001001915.1	NP_001001915.1	1	2	3	2.136668	Q8NGZ5	OR2G2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.017)	1	523	+	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	0	1	hg19	c.523C>T	CCDS31092.1	0	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563482	0.45694	.	.	ENSG00000177489	ENST00000320065	T	0.00137	8.68	4.29	2.22	0.28083	4.29	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.910260	0.08981	U	0.865762	T	0.00384	0.0012	M	0.80616	2.505	0.09310	N	1	D	0.76494	0.999	D	0.65140	0.932	T	0.49872	-0.8893	10	0.54805	T	0.06	.	3.3058	0.07000	0.2201:0.5548:0.0:0.2251	.	175	Q8NGZ5	OR2G2_HUMAN	C	175	ENSP00000326349:R175C	ENSP00000326349:R175C	R	+	1	0	0	OR2G2	245818807	245818807	0.025000	0.19082	0.764000	0.31436	0.987000	0.75469	2.319000	0.43788	1.013000	0.39391	0.591000	0.81541	CGC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.557	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1	0	0	1	2	2	2	2	0	0	0	0	231	231	231	230	1	1.800000	-2.512296	1	0.560000			0	5	5	0	396	387	0		1			0	0	231	0	0	0.934116	0	0	0	0	0	0	5	396
PMEPA1	56937	broad.mit.edu	37	20	56234669	56234669	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr20:56234669T>C	ENST00000341744.3	-	2	513	c.194A>G	c.(193-195)tAc>tGc	p.Y65C	PMEPA1_ENST00000347215.4_Missense_Mutation_p.Y30C|PMEPA1_ENST00000472841.1_5'UTR|PMEPA1_ENST00000395814.1_Missense_Mutation_p.Y15C|PMEPA1_ENST00000395816.3_Missense_Mutation_p.Y15C|PMEPA1_ENST00000265626.4_Missense_Mutation_p.Y15C	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	65					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						AGACAGCTTGTAGTGGCTCAG	0.577																																						ENST00000341744.3	1.000000	6.700000e-01	1.000000	0.830000	0.990000	0.938576	0.990000	1.000000																										0				16						c.(193-195)tAc>tGc		prostate transmembrane protein, androgen induced 1							98.0	68.0	79.0					20																	56234669		2203	4300	6503	SO:0001583	missense	56937	0	0					g.chr20:56234669T>C	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"""solid tumor-associated 1"""	606564	"""transmembrane, prostate androgen induced RNA"""	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.194A>G	chr20.hg19:g.56234669T>C	ENSP00000345826:p.Tyr65Cys	0					PMEPA1_ENST00000395814.1_Missense_Mutation_p.Y15C|PMEPA1_ENST00000347215.4_Missense_Mutation_p.Y30C|PMEPA1_ENST00000265626.4_Missense_Mutation_p.Y15C|PMEPA1_ENST00000395816.3_Missense_Mutation_p.Y15C|PMEPA1_ENST00000472841.1_5'UTR	p.Y65C	NM_020182.4	NP_064567.2	0	0	0	2.108254	Q969W9	PMEPA_HUMAN		2	513	-			Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Missense_Mutation	SNP	ENST00000341744.3	1	1	hg19	c.194A>G	CCDS13463.1	1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185907	0.57909	.	.	ENSG00000124225	ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814;ENST00000414037;ENST00000395819	T;T;T;T;T;T;T	0.68903	-0.36;-0.24;-0.17;-0.17;-0.17;-0.14;-0.17	4.74	4.74	0.60224	4.74	4.74	0.60224	.	0.131993	0.52532	D	0.000066	T	0.81413	0.4817	M	0.78049	2.395	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.84316	0.0513	10	0.87932	D	0	-27.9109	14.2249	0.65853	0.0:0.0:0.0:1.0	.	30;65	Q5JY37;Q969W9	.;PMEPA_HUMAN	C	65;30;15;15;15;37;122	ENSP00000345826:Y65C;ENSP00000344014:Y30C;ENSP00000379161:Y15C;ENSP00000265626:Y15C;ENSP00000379159:Y15C;ENSP00000401506:Y37C;ENSP00000379164:Y122C	ENSP00000265626:Y15C	Y	-	2	0	0	PMEPA1	55668075	55668075	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	7.867000	0.87062	1.774000	0.52232	0.459000	0.35465	TAC	0.557522		TCGA-IB-AAUN-01A-12D-A38G-08	0.577	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	1	0	1	2	2	2	2	0	0	0	0	48	48	48	48	1	1.800000	-20.000000	1	0.560000	NM_020182		0	19	18	0	47	47	1		1	1		0	0	48	0	0	0.999997	1	0	268	0	472	0	19	47
CSF2RB	1439	broad.mit.edu	37	22	37326748	37326748	+	Silent	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr22:37326748G>A	ENST00000403662.3	+	8	1110	c.888G>A	c.(886-888)ggG>ggA	p.G296G	CSF2RB_ENST00000406230.1_Silent_p.G302G|CSF2RB_ENST00000262825.5_Silent_p.G302G|CSF2RB_ENST00000536485.1_Silent_p.G243G			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	296					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	TGAGGGAGGGGCTCGGCAGCC	0.657																																						ENST00000403662.3	1.000000	6.800000e-01	1.000000	0.790000	0.910000	0.902919	0.910000	1.000000																										0				42						c.(886-888)ggG>ggA		colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	Sargramostim(DB00020)						43.0	40.0	41.0					22																	37326748		2203	4300	6503	SO:0001819	synonymous_variant	1439	0	0					g.chr22:37326748G>A	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.888G>A	chr22.hg19:g.37326748G>A		0					CSF2RB_ENST00000262825.5_Silent_p.G302G|CSF2RB_ENST00000536485.1_Silent_p.G243G|CSF2RB_ENST00000406230.1_Silent_p.G302G	p.G296G			1	2	3	2.175080	P32927	IL3RB_HUMAN		8	1110	+			Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	1	1	hg19	c.888G>A	CCDS13936.1	1																																																																																								0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.657	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	1	0	1	2	2	2	2	0	0	0	0	77	77	77	76	1	1.800000	-20.000000	1	0.560000	NM_000395		0	43	42	0	128	122	1		1	0		0	0	77	0	0	1.000000	7.031130e-01	0	0	0	9	0	43	128
TTLL12	23170	broad.mit.edu	37	22	43575882	43575882	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr22:43575882G>A	ENST00000216129.6	-	4	734	c.671C>T	c.(670-672)aCg>aTg	p.T224M		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	224					cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				CCACAGCAGCGTGTAGGCCAC	0.657																																						ENST00000216129.6	1.000000	2.000000e-02	0.160000	0.050000	0.090000	0.141172	0.090000	0.090000																										0				13						c.(670-672)aCg>aTg		tubulin tyrosine ligase-like family, member 12							51.0	45.0	47.0					22																	43575882		2203	4300	6503	SO:0001583	missense	23170	3	121392	34				g.chr22:43575882G>A	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.671C>T	chr22.hg19:g.43575882G>A	ENSP00000216129:p.Thr224Met	0						p.T224M	NM_015140.3	NP_055955.1	1	2	3	2.175080	Q14166	TTL12_HUMAN		4	734	-		Ovarian(80;0.221)|Glioma(61;0.222)	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	0	1	hg19	c.671C>T	CCDS14047.1	0	.	.	.	.	.	.	.	.	.	.	G	19.87	3.906526	0.72868	.	.	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.54479	0.57	5.55	5.55	0.83447	5.55	5.55	0.83447	.	0.057372	0.64402	D	0.000001	T	0.63426	0.2510	M	0.77820	2.39	0.58432	D	0.999999	D;D	0.53462	0.96;0.96	P;P	0.46237	0.508;0.508	T	0.70590	-0.4830	10	0.87932	D	0	-2.0841	19.5034	0.95105	0.0:0.0:1.0:0.0	.	224;224	B1AH89;Q14166	.;TTL12_HUMAN	M	224	ENSP00000216129:T224M	ENSP00000216129:T224M	T	-	2	0	0	TTLL12	41905826	41905826	1.000000	0.71417	1.000000	0.80357	0.206000	0.24218	9.272000	0.95707	2.593000	0.87608	0.655000	0.94253	ACG	0.566075		TCGA-IB-AAUN-01A-12D-A38G-08	0.657	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	0	0	1	2	2	2	2	0	0	0	0	98	98	98	96	1	1.800000	-6.461489	1	0.560000	NM_015140		0	4	4	0	162	159	0		1	0		0	0	98	0	0	0.887017	6.380330e-01	0	1	0	80	0	4	162
TACR1	6869	broad.mit.edu	37	2	75425709	75425709	+	Missense_Mutation	SNP	C	C	T	rs199510054		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr2:75425709C>T	ENST00000305249.5	-	1	1117	c.352G>A	c.(352-354)Gcc>Acc	p.A118T	TACR1_ENST00000409848.3_Missense_Mutation_p.A118T	NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	118					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	TAGATACTGGCGAAGACAGCG	0.498																																					Pancreas(64;62 1268 3653 14826 43765)	ENST00000305249.5	0.150000	3.000000e-02	0.120000	0.050000	0.070000	0.087379	0.070000	0.080000																										0				24						c.(352-354)Gcc>Acc		tachykinin receptor 1	Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)						121.0	112.0	115.0					2																	75425709		2203	4300	6503	SO:0001583	missense	6869	0	0					g.chr2:75425709C>T	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"""GPCR / Class A : Tachykinin receptors"""	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.352G>A	chr2.hg19:g.75425709C>T	ENSP00000303522:p.Ala118Thr	0					TACR1_ENST00000409848.3_Missense_Mutation_p.A118T	p.A118T	NM_001058.3	NP_001049.1	0	0	0	2.108370	P25103	NK1R_HUMAN		1	1117	-			A8K150	Missense_Mutation	SNP	ENST00000305249.5	0	1	hg19	c.352G>A	CCDS1958.1	0	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001310	0.74818	.	.	ENSG00000115353	ENST00000305249;ENST00000409848	T;T	0.76060	-0.99;-0.99	5.41	5.41	0.78517	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	0.049231	0.85682	D	0.000000	T	0.66684	0.2814	L	0.51914	1.62	0.80722	D	1	P	0.47604	0.898	B	0.39660	0.306	T	0.67225	-0.5724	10	0.37606	T	0.19	.	11.5873	0.50925	0.1776:0.8224:0.0:0.0	.	118	P25103	NK1R_HUMAN	T	118	ENSP00000303522:A118T;ENSP00000386448:A118T	ENSP00000303522:A118T	A	-	1	0	0	TACR1	75279217	75279217	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	4.545000	0.60698	2.798000	0.96311	0.655000	0.94253	GCC	0.557522		TCGA-IB-AAUN-01A-12D-A38G-08	0.498	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	0	0	1	2	2	2	2	0	0	0	0	193	193	193	192	1	1.800000	-2.630091	1	0.560000	NM_001058		0	8	8	0	355	348	0		1	0		0	0	193	0	0	0.988824	6.700317e-04	0	0	0	2	0	8	355
FNDC3B	64778	broad.mit.edu	37	3	172096148	172096148	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr3:172096148G>A	ENST00000336824.4	+	24	3196	c.3097G>A	c.(3097-3099)Gca>Aca	p.A1033T	FNDC3B_ENST00000415807.2_Missense_Mutation_p.A1033T|FNDC3B_ENST00000416957.1_Missense_Mutation_p.A1033T	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1033	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AATCCAGGCAGCAAGCGAGGC	0.483																																						ENST00000336824.4	0.150000	1.000000e-02	0.110000	0.030000	0.060000	0.077647	0.060000	0.060000																										0				69						c.(3097-3099)Gca>Aca		fibronectin type III domain containing 3B							88.0	87.0	87.0					3																	172096148		2203	4300	6503	SO:0001583	missense	64778	1	121412	28				g.chr3:172096148G>A	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.3097G>A	chr3.hg19:g.172096148G>A	ENSP00000338523:p.Ala1033Thr	0					FNDC3B_ENST00000415807.2_Missense_Mutation_p.A1033T|FNDC3B_ENST00000416957.1_Missense_Mutation_p.A1033T	p.A1033T	NM_001135095.1	NP_001128567.1	0	0	0	2.118878	Q53EP0	FND3B_HUMAN	LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	24	3196	+	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	0	1	hg19	c.3097G>A	CCDS3217.1	0	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830279	0.50845	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.57273	0.41;0.41;0.41	5.26	4.37	0.52481	5.26	4.37	0.52481	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.215889	0.47852	N	0.000204	T	0.27629	0.0679	N	0.02916	-0.46	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05241	-1.0897	10	0.23302	T	0.38	-5.2768	12.8682	0.57951	0.0801:0.0:0.9199:0.0	.	1033	Q53EP0	FND3B_HUMAN	T	1033	ENSP00000411242:A1033T;ENSP00000338523:A1033T;ENSP00000389094:A1033T	ENSP00000338523:A1033T	A	+	1	0	0	FNDC3B	173578842	173578842	0.862000	0.29867	0.667000	0.29798	0.980000	0.70556	1.874000	0.39568	1.183000	0.42943	0.655000	0.94253	GCA	0.560000		TCGA-IB-AAUN-01A-12D-A38G-08	0.483	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	0	0	1	2	2	2	2	0	0	0	0	100	100	100	98	1	1.800000	-3.057399	1	0.560000	NM_022763		0	4	4	0	223	216	0		1	0		0	0	100	0	0	0.883641	5.539570e-01	0	0	0	92	0	4	223
UGT8	7368	broad.mit.edu	37	4	115597336	115597336	+	Silent	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr4:115597336G>A	ENST00000310836.6	+	6	2040	c.1518G>A	c.(1516-1518)ctG>ctA	p.L506L	UGT8_ENST00000394511.3_Silent_p.L506L	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	506					axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		TCAAAAGTCTGTGGTCTAGAA	0.353																																						ENST00000310836.6	0.780000	4.900000e-01	0.700000	0.550000	0.620000	0.634075	0.620000	0.630000																										0				31						c.(1516-1518)ctG>ctA		UDP glycosyltransferase 8							84.0	78.0	80.0					4																	115597336		2203	4300	6503	SO:0001819	synonymous_variant	7368	0	0					g.chr4:115597336G>A	AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"""UDP glucuronosyltransferases"""	12555	protein-coding gene	gene with protein product	"""2-hydroxyacylsphingosine 1-beta-galactosyltransferase"""	601291	"""UDP-galactose ceramide galactosyltransferase"""	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.1518G>A	chr4.hg19:g.115597336G>A		0					UGT8_ENST00000394511.3_Silent_p.L506L	p.L506L	NM_001128174.1	NP_001121646	1	2	3	2.131604	Q16880	CGT_HUMAN		6	2040	+		Ovarian(17;0.156)	B3KXU7|O00196	Silent	SNP	ENST00000310836.6	1	1	hg19	c.1518G>A	CCDS3705.1	0																																																																																								0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.353	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	1	0	1	2	2	2	2	0	0	0	0	190	190	190	189	1	1.800000	-20.000000	1	0.560000	NM_003360		0	65	63	0	305	298	1		1	1		0	0	190	0	0	1.000000	8.250520e-01	0	4	0	13	0	65	305
FAT4	79633	broad.mit.edu	37	4	126372375	126372375	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr4:126372375C>T	ENST00000394329.3	+	9	10217	c.10204C>T	c.(10204-10206)Ccc>Tcc	p.P3402S	FAT4_ENST00000335110.5_Missense_Mutation_p.P1700S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3402	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AAATGACCCACCCATTTTTAC	0.458																																						ENST00000394329.3	0.120000	2.000000e-02	0.090000	0.040000	0.060000	0.073339	0.060000	0.070000																										0				355						c.(10204-10206)Ccc>Tcc		FAT atypical cadherin 4							185.0	176.0	179.0					4																	126372375		2203	4300	6503	SO:0001583	missense	79633	0	0					g.chr4:126372375C>T	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10204C>T	chr4.hg19:g.126372375C>T	ENSP00000377862:p.Pro3402Ser	0					FAT4_ENST00000335110.5_Missense_Mutation_p.P1700S	p.P3402S	NM_024582.4	NP_078858.4	1	2	3	2.131604	Q6V0I7	FAT4_HUMAN		9	10217	+			A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	0	1	hg19	c.10204C>T	CCDS3732.3	0	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665933	0.67700	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	D;D	0.84800	-1.9;-1.9	5.14	5.14	0.70334	5.14	5.14	0.70334	Cadherin (3);Cadherin-like (1);	0.000000	0.34362	U	0.004026	D	0.95500	0.8538	H	0.97440	4.005	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.97;0.998	D	0.97250	0.9897	10	0.87932	D	0	.	18.629	0.91352	0.0:1.0:0.0:0.0	.	1700;3402;3402	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	S	3402;1700	ENSP00000377862:P3402S;ENSP00000335169:P1700S	ENSP00000335169:P1700S	P	+	1	0	0	FAT4	126591825	126591825	1.000000	0.71417	0.944000	0.38274	0.741000	0.42261	7.662000	0.83803	2.392000	0.81423	0.561000	0.74099	CCC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.458	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	0	0	1	2	2	2	2	0	0	0	0	329	329	329	328	1	1.800000	-2.905452	1	0.560000	NM_024582		0	12	12	0	620	608	0		1	0		0	0	329	0	0	0.999015	4.311475e-03	0	0	0	5	0	12	620
SLC12A7	10723	broad.mit.edu	37	5	1064314	1064314	+	Missense_Mutation	SNP	C	C	T	rs188889163	byFrequency	TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr5:1064314C>T	ENST00000264930.5	-	19	2534	c.2491G>A	c.(2491-2493)Gtc>Atc	p.V831I	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	831					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	AACGAGTCGACGTTCTTGGCC	0.677													C|||	2	0.000399361	0.0008	0.0	5008	,	,		13721	0.001		0.0	False		,,,				2504	0.0					ENST00000264930.5	1.000000	7.400000e-01	1.000000	0.860000	0.980000	0.945383	0.980000	1.000000																										0				32						c.(2491-2493)Gtc>Atc		solute carrier family 12 (potassium/chloride transporter), member 7	Potassium Chloride(DB00761)	C	ILE/VAL	1,4387	2.1+/-5.4	0,1,2193	37.0	40.0	39.0		2491	-0.3	1.0	5		39	0,8596		0,0,4298	no	missense	SLC12A7	NM_006598.2	29	0,1,6491	TT,TC,CC		0.0,0.0228,0.0077	benign	831/1084	1064314	1,12983	2194	4298	6492	SO:0001583	missense	10723	4	120850	35				g.chr5:1064314C>T	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2491G>A	chr5.hg19:g.1064314C>T	ENSP00000264930:p.Val831Ile	0					MIR4635_ENST00000583759.1_RNA	p.V831I	NM_006598.2	NP_006589.2	1	2	3	2.129760	Q9Y666	S12A7_HUMAN	Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)	19	2534	-	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	1	1	hg19	c.2491G>A	CCDS34129.1	1	2|2	9.157509157509158E-4|9.157509157509158E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	C|C	0.018|0.018	-1.479004|-1.479004	0.01035|0.01035	2.28E-4|2.28E-4	0.0|0.0	ENSG00000113504|ENSG00000113504	ENST00000513223|ENST00000264930	.|D	.|0.86432	.|-2.12	4.26|4.26	-0.302|-0.302	0.12796|0.12796	4.26|4.26	-0.302|-0.302	0.12796|0.12796	.|.	.|0.562347	.|0.17891	.|N	.|0.158521	T|T	0.61324|0.61324	0.2338|0.2338	N|N	0.02286|0.02286	-0.61|-0.61	0.28050|0.28050	N|N	0.933393|0.933393	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.55885|0.55885	-0.8070|-0.8070	5|10	.|0.02654	.|T	.|1	.|.	7.5601|7.5601	0.27847|0.27847	0.0:0.37:0.0:0.63|0.0:0.37:0.0:0.63	.|.	.|831	.|Q9Y666	.|S12A7_HUMAN	H|I	188|831	.|ENSP00000264930:V831I	.|ENSP00000264930:V831I	R|V	-|-	2|1	0|0	0|0	SLC12A7|SLC12A7	1117314|1117314	1117314|1117314	0.943000|0.943000	0.32029|0.32029	0.959000|0.959000	0.39883|0.39883	0.022000|0.022000	0.10575|0.10575	0.148000|0.148000	0.16224|0.16224	0.072000|0.072000	0.16694|0.16694	-0.657000|-0.657000	0.03884|0.03884	CGT|GTC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.677	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	1	0	1	2	2	2	2	0	0	0	0	102	102	102	99	1	1.800000	-20.000000	1	0.560000	NM_006598		0	43	41	0	113	109	0		1	1		0	0	102	0	0	1.000000	1	0	47	0	49	0	43	113
PCDHA1	56147	broad.mit.edu	37	5	140167552	140167552	+	Silent	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr5:140167552C>T	ENST00000504120.2	+	1	1677	c.1677C>T	c.(1675-1677)aaC>aaT	p.N559N	PCDHA1_ENST00000378133.3_Silent_p.N559N|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	559	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGACGAGAACGACAACGCGC	0.672																																						ENST00000504120.2	1.000000	8.200000e-01	1.000000	0.880000	0.940000	0.944873	0.940000	1.000000																										0				70						c.(1675-1677)aaC>aaT		protocadherin alpha 1							86.0	87.0	87.0					5																	140167552		2203	4299	6502	SO:0001819	synonymous_variant	56147	0	0					g.chr5:140167552C>T	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1677C>T	chr5.hg19:g.140167552C>T		0					PCDHA1_ENST00000378133.3_Silent_p.N559N|PCDHA1_ENST00000394633.3_Intron	p.N559N	NM_018900.2	NP_061723.1	1	2	3	2.131117	Q9Y5I3	PCDA1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	1	1677	+			O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	1	1	hg19	c.1677C>T	CCDS54913.1	1																																																																																								0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.672	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	1	0	1	2	9	2	2	0	0	0	1	285	285	285	294	1	1.800000	-20.000000	1	0.560000	NM_018900		0	147	143	0	405	394	1		1			0	0	285	0	0	1.000000	0	0	0	0	0	0	147	405
ITGA2	3673	broad.mit.edu	37	5	52360796	52360796	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr5:52360796C>T	ENST00000296585.5	+	14	1800	c.1657C>T	c.(1657-1659)Cga>Tga	p.R553*		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	553					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TGAAAACACTCGATTTGGTTC	0.423																																						ENST00000296585.5	1.000000	7.600000e-01	0.970000	0.830000	0.890000	0.899938	0.890000	1.000000																										0				47						c.(1657-1659)Cga>Tga		integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)							150.0	148.0	149.0					5																	52360796		2203	4300	6503	SO:0001587	stop_gained	3673	0	0					g.chr5:52360796C>T		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.1657C>T	chr5.hg19:g.52360796C>T	ENSP00000296585:p.Arg553*	0						p.R553*	NM_002203.3	NP_002194.2	1	2	3	2.129760	P17301	ITA2_HUMAN		14	1800	+		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)	Q14595	Nonsense_Mutation	SNP	ENST00000296585.5	0	1	hg19	c.1657C>T	CCDS3957.1	1	.	.	.	.	.	.	.	.	.	.	C	38	6.920610	0.97936	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.67	2.83	0.33086	5.67	2.83	0.33086	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0088	0.71533	0.3736:0.6264:0.0:0.0	.	.	.	.	X	553	.	ENSP00000296585:R553X	R	+	1	2	2	ITGA2	52396553	52396553	0.972000	0.33761	0.988000	0.46212	0.995000	0.86356	2.181000	0.42547	0.371000	0.24564	0.655000	0.94253	CGA	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.423	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	1	0	1	2	2	2	2	0	0	0	0	282	282	282	275	1	1.800000	-20.000000	1	0.560000	NM_002203		0	135	135	0	402	394	1		1	0		0	0	282	0	0	1.000000	9.991600e-01	0	1	0	33	0	135	402
FGF18	8817	broad.mit.edu	37	5	170876235	170876235	+	Missense_Mutation	SNP	G	G	A	rs201988531		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr5:170876235G>A	ENST00000274625.5	+	4	879	c.335G>A	c.(334-336)cGc>cAc	p.R112H		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	112					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGCATGAACCGCAAAGGCAAG	0.567													g|||	1	0.000199681	0.0	0.0	5008	,	,		16702	0.0		0.001	False		,,,				2504	0.0					ENST00000274625.5	0.140000	1.000000e-02	0.100000	0.030000	0.060000	0.071914	0.060000	0.060000																										0				9						c.(334-336)cGc>cAc		fibroblast growth factor 18							112.0	89.0	97.0					5																	170876235		2203	4300	6503	SO:0001583	missense	8817	3	121412	36				g.chr5:170876235G>A	AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.335G>A	chr5.hg19:g.170876235G>A	ENSP00000274625:p.Arg112His	0						p.R112H	NM_003862.2	NP_003853.1	1	2	3	2.131117	O76093	FGF18_HUMAN	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	4	879	+	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	D3DQL7|Q6UWF1	Missense_Mutation	SNP	ENST00000274625.5	0	1	hg19	c.335G>A	CCDS4378.1	0	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	21.3	4.124259	0.77436	.	.	ENSG00000156427	ENST00000274625	D	0.89343	-2.5	4.08	3.19	0.36642	4.08	3.19	0.36642	.	0.556585	0.16736	U	0.201631	D	0.90769	0.7102	M	0.77820	2.39	0.25546	N	0.987134	D	0.55605	0.972	P	0.53809	0.735	T	0.83312	-0.0022	10	0.72032	D	0.01	-2.8976	6.6409	0.22909	0.0934:0.0:0.7276:0.1789	.	112	O76093	FGF18_HUMAN	H	112	ENSP00000274625:R112H	ENSP00000274625:R112H	R	+	2	0	0	FGF18	170808840	170808840	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	4.443000	0.59994	0.688000	0.31529	0.450000	0.29827	CGC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.567	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252857.2	0	0	1	2	2	2	2	0	0	0	0	156	156	156	154	1	1.800000	-2.293342	0	0.560000	NM_033649, NM_003862		0	5	5	0	291	284	0		1	0		0	0	156	0	0	0.933476	8.999583e-03	0	0	0	7	0	5	291
MAPK13	5603	broad.mit.edu	37	6	36106684	36106684	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr6:36106684G>C	ENST00000211287.4	+	11	1132	c.870G>C	c.(868-870)gaG>gaC	p.E290D	MAPK13_ENST00000373766.5_Missense_Mutation_p.A240P|Z95152.1_ENST00000408816.1_RNA|MAPK13_ENST00000373761.6_Missense_Mutation_p.E280D|MAPK13_ENST00000373759.1_3'UTR	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						AGATGCTGGAGCTAGACGTGG	0.667																																						ENST00000211287.4	1.000000	7.700000e-01	1.000000	0.890000	0.990000	0.961069	0.990000	1.000000																										0				12						c.(868-870)gaG>gaC		mitogen-activated protein kinase 13							43.0	46.0	45.0					6																	36106684		2203	4300	6503	SO:0001583	missense	5603	0	0					g.chr6:36106684G>C	Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.870G>C	chr6.hg19:g.36106684G>C	ENSP00000211287:p.Glu290Asp	0					MAPK13_ENST00000373766.5_Missense_Mutation_p.A240P|MAPK13_ENST00000373759.1_3'UTR|MAPK13_ENST00000373761.6_Missense_Mutation_p.E280D|Z95152.1_ENST00000408816.1_RNA	p.E290D	NM_002754.4	NP_002745.1	0	1	1	2.114030	O15264	MK13_HUMAN		11	1132	+			O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Missense_Mutation	SNP	ENST00000211287.4	1	1	hg19	c.870G>C	CCDS4818.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.12|13.12	2.143296|2.143296	0.37825|0.37825	.|.	.|.	ENSG00000156711|ENSG00000156711	ENST00000373766|ENST00000373761;ENST00000211287;ENST00000373770	T|T;T	0.66995|0.65364	-0.24|-0.15;-0.15	5.25|5.25	3.47|3.47	0.39725|0.39725	5.25|5.25	3.47|3.47	0.39725|0.39725	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.105229	.|0.41605	.|D	.|0.000844	T|T	0.29684|0.29684	0.0741|0.0741	L|L	0.33245|0.33245	0.995|0.995	0.23632|0.23632	N|N	0.997245|0.997245	.|B	.|0.09022	.|0.002	.|B	.|0.09377	.|0.004	T|T	0.21827|0.21827	-1.0234|-1.0234	7|10	0.72032|0.42905	D|T	0.01|0.14	-45.63|-45.63	11.297|11.297	0.49284|0.49284	0.1481:0.0:0.8519:0.0|0.1481:0.0:0.8519:0.0	.|.	.|290	.|O15264	.|MK13_HUMAN	P|D	240|280;290;235	ENSP00000362871:A240P|ENSP00000362866:E280D;ENSP00000211287:E290D	ENSP00000362871:A240P|ENSP00000211287:E290D	A|E	+|+	1|3	0|2	0|2	MAPK13|MAPK13	36214662|36214662	36214662|36214662	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.831000|0.831000	0.47069|0.47069	1.350000|1.350000	0.34010|0.34010	0.605000|0.605000	0.29947|0.29947	0.484000|0.484000	0.47621|0.47621	GCT|GAG	0.558765		TCGA-IB-AAUN-01A-12D-A38G-08	0.667	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1	1	0	1	2	2	2	2	0	0	0	0	84	84	84	83	1	1.800000	-20.000000	1	0.560000			0	45	45	0	112	110	1		1	1		0	0	84	0	0	1.000000	1	0	26	0	107	0	45	112
HOXA3	3200	broad.mit.edu	37	7	27148046	27148046	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr7:27148046C>T	ENST00000396352.4	-	3	1019	c.820G>A	c.(820-822)Ggt>Agt	p.G274S	HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank|HOXA3_ENST00000317201.2_Missense_Mutation_p.G274S	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	274					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						AGATAGCCACCGGCTCCGGGG	0.627																																					Esophageal Squamous(136;1368 1743 5685 7935 50360)	ENST00000396352.4	0.970000	6.600000e-01	0.900000	0.730000	0.810000	0.820510	0.810000	0.820000																										0				29						c.(820-822)Ggt>Agt		homeobox A3							86.0	88.0	88.0					7																	27148046		2203	4300	6503	SO:0001583	missense	3200	0	0					g.chr7:27148046C>T		CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"""Homeoboxes / ANTP class : HOXL subclass"""	5104	protein-coding gene	gene with protein product		142954	"""homeo box A3"""	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.820G>A	chr7.hg19:g.27148046C>T	ENSP00000379640:p.Gly274Ser	0					HOXA3_ENST00000317201.2_Missense_Mutation_p.G274S|HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank	p.G274S	NM_030661.4	NP_109377.1	0	0	0	2.116104	O43365	HXA3_HUMAN		3	1019	-			A4D181	Missense_Mutation	SNP	ENST00000396352.4	1	1	hg19	c.820G>A	CCDS5404.1	0	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340433	0.41498	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.86297	-2.1;-2.1	5.41	5.41	0.78517	5.41	5.41	0.78517	.	0.047410	0.85682	D	0.000000	D	0.91955	0.7452	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90337	0.4356	10	0.33940	T	0.23	.	19.215	0.93772	0.0:1.0:0.0:0.0	.	274	O43365	HXA3_HUMAN	S	274;274;116	ENSP00000379640:G274S;ENSP00000324884:G274S	ENSP00000324884:G274S	G	-	1	0	0	HOXA3	27114571	27114571	1.000000	0.71417	0.432000	0.26747	0.546000	0.35178	6.089000	0.71384	2.539000	0.85634	0.655000	0.94253	GGT	0.560000		TCGA-IB-AAUN-01A-12D-A38G-08	0.627	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2	0	0	1	2	9	2	2	1	1	1	1	193	193	193	190	1	1.800000	-4.020497	1	0.560000			0	84	82	0	283	270	0		1	0		1	0	193	0	0	1.000000	8.326117e-01	0	1	0	12	0	84	283
SCARA5	286133	broad.mit.edu	37	8	27737142	27737142	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr8:27737142C>T	ENST00000354914.3	-	8	1780	c.1295G>A	c.(1294-1296)cGc>cAc	p.R432H	SCARA5_ENST00000380385.2_Missense_Mutation_p.R207H	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	432	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		GCCGAGCATGCGGCACACCAC	0.642																																						ENST00000354914.3	0.100000	1.000000e-02	0.070000	0.020000	0.040000	0.054242	0.040000	0.050000																										0				18						c.(1294-1296)cGc>cAc		scavenger receptor class A, member 5							156.0	121.0	133.0					8																	27737142		2203	4300	6503	SO:0001583	missense	286133	0	0					g.chr8:27737142C>T	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.1295G>A	chr8.hg19:g.27737142C>T	ENSP00000346990:p.Arg432His	1					SCARA5_ENST00000380385.2_Missense_Mutation_p.R207H	p.R432H	NM_173833.5	NP_776194.2	0	1	1	1.575933	Q6ZMJ2	SCAR5_HUMAN		8	1780	-		Ovarian(32;0.0218)	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	0	1	hg19	c.1295G>A	CCDS6064.1	0	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480662	0.63849	.	.	ENSG00000168079	ENST00000354914;ENST00000380385	T;T	0.42900	0.96;0.96	4.87	3.99	0.46301	4.87	3.99	0.46301	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.063343	0.64402	N	0.000010	T	0.48804	0.1520	M	0.88241	2.94	0.80722	D	1	B;B	0.25206	0.012;0.12	B;B	0.19946	0.008;0.027	T	0.54417	-0.8297	10	0.66056	D	0.02	.	11.0431	0.47842	0.0:0.907:0.0:0.093	.	207;432	Q6ZMJ2-4;Q6ZMJ2	.;SCAR5_HUMAN	H	432;207	ENSP00000346990:R432H;ENSP00000369746:R207H	ENSP00000346990:R432H	R	-	2	0	0	SCARA5	27793061	27793061	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	4.882000	0.63121	1.170000	0.42753	0.591000	0.81541	CGC	0.391256		TCGA-IB-AAUN-01A-12D-A38G-08	0.642	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	0	0	1	2	2	2	2	0	0	0	0	171	171	171	169	1	1.800000	-2.163064	0	0.560000	NM_173833		0	5	4	0	277	273	0		1	0		0	0	171	0	0	0.936322	0	0	0	0	1	0	5	277
UNC5D	137970	broad.mit.edu	37	8	35608224	35608224	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr8:35608224C>T	ENST00000404895.2	+	13	2388	c.2060C>T	c.(2059-2061)gCc>gTc	p.A687V	UNC5D_ENST00000287272.2_Missense_Mutation_p.A618V|UNC5D_ENST00000420357.1_Missense_Mutation_p.A620V|UNC5D_ENST00000416672.1_Missense_Mutation_p.A692V|UNC5D_ENST00000453357.2_Missense_Mutation_p.A682V|UNC5D_ENST00000449677.1_Missense_Mutation_p.A263V	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	687					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.A682V(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ACAGACTGTGCCGTGAAGCAA	0.502																																						ENST00000404895.2	0.070000	0	0.050000	0.010000	0.030000	0.038005	0.030000	0.030000																										1	Substitution - Missense(1)	p.A682V(1)	prostate(1)	112						c.(2059-2061)gCc>gTc		unc-5 homolog D (C. elegans)							253.0	210.0	225.0					8																	35608224		2203	4300	6503	SO:0001583	missense	137970	0	0					g.chr8:35608224C>T	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.2060C>T	chr8.hg19:g.35608224C>T	ENSP00000385143:p.Ala687Val	1					UNC5D_ENST00000287272.2_Missense_Mutation_p.A618V|UNC5D_ENST00000449677.1_Missense_Mutation_p.A263V|UNC5D_ENST00000453357.2_Missense_Mutation_p.A682V|UNC5D_ENST00000416672.1_Missense_Mutation_p.A692V|UNC5D_ENST00000420357.1_Missense_Mutation_p.A620V	p.A687V	NM_080872.2	NP_543148.2	0	1	1	1.575933	Q6UXZ4	UNC5D_HUMAN		13	2388	+			Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	0	1	hg19	c.2060C>T	CCDS6093.2	0	.	.	.	.	.	.	.	.	.	.	C	35	5.426783	0.96131	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677	T;T;T;T;T;T	0.60299	0.23;0.64;0.63;0.23;0.2;2.1	5.9	5.9	0.94986	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	M	0.83483	2.645	0.80722	D	1	D;P;P	0.56035	0.974;0.911;0.914	P;P;B	0.50490	0.638;0.642;0.439	T	0.76817	-0.2819	10	0.87932	D	0	-23.3889	20.2822	0.98520	0.0:1.0:0.0:0.0	.	263;682;687	E9PDS8;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	V	687;620;618;692;682;263	ENSP00000385143:A687V;ENSP00000392739:A620V;ENSP00000287272:A618V;ENSP00000412652:A692V;ENSP00000394303:A682V;ENSP00000397211:A263V	ENSP00000287272:A618V	A	+	2	0	0	UNC5D	35727766	35727766	1.000000	0.71417	0.987000	0.45799	0.959000	0.62525	5.359000	0.66074	2.806000	0.96561	0.655000	0.94253	GCC	0.391256		TCGA-IB-AAUN-01A-12D-A38G-08	0.502	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2	0	0	1	2	2	2	2	0	0	0	0	297	297	297	296	1	1.800000	-1.885794	0	0.560000			0	5	5	0	399	386	0		1			0	0	297	0	0	0.932385	0	0	0	0	0	0	5	399
KCNQ3	3786	broad.mit.edu	37	8	133141815	133141815	+	Silent	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr8:133141815C>T	ENST00000388996.4	-	15	2733	c.2313G>A	c.(2311-2313)tcG>tcA	p.S771S	KCNQ3_ENST00000521134.1_Silent_p.S651S|KCNQ3_ENST00000519445.1_Silent_p.S759S	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	771					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	AGATTCGGTCCGAGTAGGGGC	0.607																																						ENST00000388996.4	1.000000	4.000000e-02	0.220000	0.080000	0.130000	0.195299	0.130000	0.120000																										0				70						c.(2311-2313)tcG>tcA		potassium voltage-gated channel, KQT-like subfamily, member 3	Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)						45.0	45.0	45.0					8																	133141815		2203	4300	6503	SO:0001819	synonymous_variant	3786	3	121412	32				g.chr8:133141815C>T	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2313G>A	chr8.hg19:g.133141815C>T		1					KCNQ3_ENST00000521134.1_Silent_p.S651S|KCNQ3_ENST00000519445.1_Silent_p.S759S	p.S771S	NM_004519.3	NP_004510.1	1	2	3	2.641472	O43525	KCNQ3_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.000311)	15	2733	-	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	0	1	hg19	c.2313G>A	CCDS34943.1	0																																																																																								0.650127		TCGA-IB-AAUN-01A-12D-A38G-08	0.607	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	0	0	1	2	2	2	2	0	0	0	0	92	92	92	92	1	1.800000	-6.791372	1	0.560000	NM_004519		0	5	5	0	185	181	0		1	0		0	0	92	0	0	0.934835	3.306781e-03	0	0	0	3	0	5	185
KDM4C	23081	broad.mit.edu	37	9	6990510	6990510	+	Missense_Mutation	SNP	C	C	T	rs151291155		TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr9:6990510C>T	ENST00000381309.3	+	12	2337	c.1772C>T	c.(1771-1773)gCg>gTg	p.A591V	KDM4C_ENST00000535193.1_Missense_Mutation_p.A613V|KDM4C_ENST00000428870.2_Missense_Mutation_p.A278V|KDM4C_ENST00000543771.1_Missense_Mutation_p.A591V|KDM4C_ENST00000536108.1_Missense_Mutation_p.A410V|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.A591V	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	591					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AAGCAGCAGGCGCCAAGTGAT	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		13775	0.0		0.001	False		,,,				2504	0.0					ENST00000381309.3	1.000000	9.900000e-01	1.000000	0.990000	0.990000	0.999402	0.990000	1.000000																										0				43						c.(1771-1773)gCg>gTg		lysine (K)-specific demethylase 4C		C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	54.0	46.0	49.0		1772,1772,1838,1772	2.9	0.8	9	dbSNP_134	49	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	64,64,64,64	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign,benign,benign,benign	591/1048,591/814,613/836,591/1057	6990510	3,13003	2203	4300	6503	SO:0001583	missense	23081	23	121398	45				g.chr9:6990510C>T	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1772C>T	chr9.hg19:g.6990510C>T	ENSP00000370710:p.Ala591Val	0					KDM4C_ENST00000536108.1_Missense_Mutation_p.A410V|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.A591V|KDM4C_ENST00000535193.1_Missense_Mutation_p.A613V|KDM4C_ENST00000543771.1_Missense_Mutation_p.A591V|KDM4C_ENST00000428870.2_Missense_Mutation_p.A278V	p.A591V	NM_015061.3	NP_055876.2	0	0	0	2.121522	Q9H3R0	KDM4C_HUMAN		12	2337	+			B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	1	1	hg19	c.1772C>T	CCDS6471.1	1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.18	2.159146	0.38119	2.27E-4	2.33E-4	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870	T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66	4.8	2.93	0.34026	4.8	2.93	0.34026	.	0.294931	0.36703	N	0.002452	T	0.31040	0.0784	L	0.35414	1.06	0.44366	D	0.997269	B;B;B;B	0.29627	0.043;0.252;0.026;0.077	B;B;B;B	0.21151	0.012;0.033;0.013;0.024	T	0.06127	-1.0844	10	0.30078	T	0.28	-39.5448	8.6521	0.34040	0.0:0.8202:0.0:0.1798	.	591;613;591;591	F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;KDM4C_HUMAN;.	V	613;591;591;591;410;278	ENSP00000442382:A613V;ENSP00000445427:A591V;ENSP00000370710:A591V;ENSP00000370707:A591V;ENSP00000440656:A410V;ENSP00000405739:A278V	ENSP00000370707:A591V	A	+	2	0	0	KDM4C	6980510	6980510	0.990000	0.36364	0.839000	0.33178	0.756000	0.42949	2.883000	0.48554	0.600000	0.29862	0.557000	0.71058	GCG	0.560000		TCGA-IB-AAUN-01A-12D-A38G-08	0.408	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	1	0	1	2	2	2	2	0	0	0	0	68	68	68	66	1	1.800000	-3.318795	1	0.560000	NM_015061		0	44	43	0	73	71	1		1	1		0	0	68	0	0	1.000000	9.961661e-01	0	2	0	16	0	44	73
HABP4	22927	broad.mit.edu	37	9	99227683	99227683	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr9:99227683C>T	ENST00000375249.4	+	3	652	c.577C>T	c.(577-579)Cgc>Tgc	p.R193C	HABP4_ENST00000375251.3_Intron	NM_014282.2	NP_055097.2			hyaluronan binding protein 4											NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				AGGGGGTATGCGCGGCAGAGG	0.483																																						ENST00000375249.4	0.110000	1.000000e-02	0.080000	0.020000	0.040000	0.055506	0.040000	0.050000																										0				13						c.(577-579)Cgc>Tgc		hyaluronan binding protein 4							101.0	114.0	109.0					9																	99227683		2203	4300	6503	SO:0001583	missense	22927	3	121412	38				g.chr9:99227683C>T	AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.577C>T	chr9.hg19:g.99227683C>T	ENSP00000364398:p.Arg193Cys	0					HABP4_ENST00000375251.3_Intron	p.R193C	NM_014282.2	NP_055097.2	1	2	3	2.124566				3	652	+		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)		Missense_Mutation	SNP	ENST00000375249.4	0	1	hg19	c.577C>T	CCDS6719.1	0	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837388	0.50951	.	.	ENSG00000130956	ENST00000375249	T	0.37752	1.18	4.86	2.77	0.32553	4.86	2.77	0.32553	.	0.269438	0.30538	N	0.009418	T	0.42381	0.1200	L	0.43923	1.385	0.49213	D	0.999769	D	0.71674	0.998	P	0.53185	0.72	T	0.40515	-0.9559	10	0.72032	D	0.01	-7.7391	14.0166	0.64527	0.4686:0.5314:0.0:0.0	.	193	Q5JVS0	HABP4_HUMAN	C	193	ENSP00000364398:R193C	ENSP00000364398:R193C	R	+	1	0	0	HABP4	98267504	98267504	1.000000	0.71417	0.350000	0.25708	0.389000	0.30415	1.202000	0.32271	0.558000	0.29135	0.644000	0.83932	CGC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.483	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	0	0	1	2	10	3	2	1	1	1	1	193	193	193	192	1	1.800000	-1.649228	0	0.560000	NM_014282		0	6	6	0	443	436	0		0	0		1	0	193	0	0	0.215731	3.750624e-02	0	1	0	43	0	6	443
ODF2	4957	broad.mit.edu	37	9	131245096	131245096	+	Splice_Site	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chr9:131245096G>A	ENST00000434106.3	+	10	1280	c.917G>A	c.(916-918)cGc>cAc	p.R306H	ODF2_ENST00000372814.3_Splice_Site_p.R350H|ODF2_ENST00000393527.3_Splice_Site_p.R282H|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000546203.1_Splice_Site_p.R287H|ODF2_ENST00000444119.2_Splice_Site_p.R282H|ODF2_ENST00000351030.3_Splice_Site_p.R301H|ODF2_ENST00000372807.5_Splice_Site_p.R301H|ODF2_ENST00000604420.1_Splice_Site_p.R306H|ODF2_ENST00000372791.3_Splice_Site_p.R287H|ODF2_ENST00000393533.2_Splice_Site_p.R306H|ODF2_ENST00000448249.3_Splice_Site_p.R225H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	306					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CTCTCCCAGCGCCTGCTGTTA	0.522																																						ENST00000434106.3	0.200000	2.000000e-02	0.140000	0.050000	0.080000	0.100145	0.080000	0.080000																										0				37						c.(916-918)cGc>cAc		outer dense fiber of sperm tails 2							66.0	72.0	70.0					9																	131245096		2203	4300	6503	SO:0001630	splice_region_variant	4957	7	121412	37				g.chr9:131245096G>A	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.916-1G>A	chr9.hg19:g.131245096G>A		0					ODF2_ENST00000351030.3_Splice_Site_p.R301H|ODF2_ENST00000546203.1_Splice_Site_p.R287H|ODF2_ENST00000444119.2_Splice_Site_p.R282H|ODF2_ENST00000393527.3_Splice_Site_p.R282H|ODF2_ENST00000604420.1_Splice_Site_p.R306H|ODF2_ENST00000448249.3_Splice_Site_p.R225H|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000372791.3_Splice_Site_p.R287H|ODF2_ENST00000372807.5_Splice_Site_p.R301H|ODF2_ENST00000393533.2_Splice_Site_p.R306H|ODF2_ENST00000372814.3_Splice_Site_p.R350H	p.R306H	NM_153433.1	NP_702911.1	1	2	3	2.132803	Q5BJF6	ODFP2_HUMAN		10	1280	+			B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Splice_Site	SNP	ENST00000434106.3	0	1	hg19	c.917G>A	CCDS56588.1	0	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854984	0.32791	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;1.87;0.93;0.93;0.93	5.66	2.68	0.31781	5.66	2.68	0.31781	.	0.552387	0.21440	N	0.074507	T	0.20333	0.0489	N	0.17474	0.49	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.27316	0.025;0.006;0.115;0.003;0.175;0.066;0.01;0.025;0.024;0.017	B;B;B;B;B;B;B;B;B;B	0.12837	0.002;0.003;0.006;0.002;0.004;0.008;0.004;0.002;0.004;0.003	T	0.05920	-1.0856	10	0.34782	T	0.22	-7.0512	3.5239	0.07752	0.3275:0.0:0.5038:0.1688	.	287;301;225;240;306;350;301;287;306;282	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;Q5BJF6-2;B4DX73;Q5BJF6-7;B1AND4;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;.;.;.;ODFP2_HUMAN;.	H	306;350;301;306;282;225;287;287	ENSP00000377166:R306H;ENSP00000361901:R350H;ENSP00000342581:R301H;ENSP00000361882:R306H;ENSP00000307781:R282H;ENSP00000396687:R225H;ENSP00000437579:R287H;ENSP00000361877:R287H	ENSP00000307781:R282H	R	+	2	0	0	ODF2	130284917	130284917	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	2.513000	0.45494	0.750000	0.32877	0.561000	0.74099	CGC	0.561229		TCGA-IB-AAUN-01A-12D-A38G-08	0.522	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3	0	0	0	2	2	2	2	0	0	0	0	95	95	95	94	1	1.800000	-5.792634	1	0.560000		Missense_Mutation	0	4	4	0	172	169	0		1	0		0	0	95	0	0	0.887246	1.987764e-01	0	0	0	29	0	4	172
ATRX	546	broad.mit.edu	37	X	76938955	76938955	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-AAUN-01A-12D-A38G-08	TCGA-IB-AAUN-10A-01D-A38J-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c613c8d-8ef7-44da-8a5f-ed1ec5652f85	15447e58-6c71-422c-ae2a-31be9bc175d5	g.chrX:76938955G>A	ENST00000373344.5	-	9	2007	c.1793C>T	c.(1792-1794)tCc>tTc	p.S598F	ATRX_ENST00000395603.3_Missense_Mutation_p.S560F|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	598					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTTAATTGGGGAATTAGAAAG	0.358			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5	1.000000	8.600000e-01	0.980000	0.890000	0.930000	0.938995	0.930000	0.940000				Rec	yes			Rec	yes		X	Xq21.1	Xq21.1	546	Mis, F, N	alpha thalassemia/mental retardation syndrome X-linked	yes	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E	E			Pancreatic neuroendocrine tumors, paediatric GBM		1	Unknown(1)	p.?(1)	bone(1)	145						c.(1792-1794)tCc>tTc		alpha thalassemia/mental retardation syndrome X-linked							194.0	222.0	213.0					X																	76938955		2203	4296	6499	SO:0001583	missense	546	0	0					g.chrX:76938955G>A	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1793C>T	chrX.hg19:g.76938955G>A	ENSP00000362441:p.Ser598Phe						ATRX_ENST00000395603.3_Missense_Mutation_p.S560F|ATRX_ENST00000480283.1_5'UTR	p.S598F	NM_000489.3	NP_000480.3	0	1	1		P46100	ATRX_HUMAN		9	2007	-			D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	1	1	hg19	c.1793C>T	CCDS14434.1	1	.	.	.	.	.	.	.	.	.	.	g	12.65	2.001168	0.35320	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.93019	-3.13;-3.15	5.22	5.22	0.72569	5.22	5.22	0.72569	.	0.000000	0.52532	D	0.000066	D	0.95774	0.8625	L	0.53249	1.67	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.78314	0.939;0.991	D	0.96302	0.9222	10	0.72032	D	0.01	-2.9111	17.9679	0.89105	0.0:0.0:1.0:0.0	.	560;598	P46100-4;P46100	.;ATRX_HUMAN	F	598;560	ENSP00000362441:S598F;ENSP00000378967:S560F	ENSP00000362441:S598F	S	-	2	0	0	ATRX	76825611	76825611	1.000000	0.71417	0.987000	0.45799	0.962000	0.63368	4.326000	0.59241	2.177000	0.69029	0.509000	0.49947	TCC	0.560000		TCGA-IB-AAUN-01A-12D-A38G-08	0.358	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	1	0	1	2	13	2	2	1	1	1	2	896	896	896	888	1	1.800000	-20.000000	1	0.560000	NM_000489		0	495	488	0	1387	1363	1		1	0		1	0	896	0	0	1.000000	9.813111e-01	0	0	0	20	0	495	1387
