#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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AFF2	2334	broad.mit.edu;ucsc.edu	37	X	148037884	148037884	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chrX:148037884C>T	ENST00000370460.2	+	11	2788	c.2309C>T	c.(2308-2310)tCc>tTc	p.S770F	AFF2_ENST00000342251.3_Missense_Mutation_p.S737F|AFF2_ENST00000370457.5_Missense_Mutation_p.S737F|AFF2_ENST00000286437.5_Missense_Mutation_p.S411F	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	770					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.S770F(2)|p.S411F(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AACAACTTATCCATCAGTAAT	0.453																																																	3	Substitution - Missense(3)	kidney(3)											105.0	93.0	97.0					X																	148037884		2203	4300	6503	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2309C>T	X.37:g.148037884C>T	ENSP00000359489:p.Ser770Phe		A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.458242	0.26161	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.63	4.74	0.60224	.	1.500750	0.03598	N	0.233000	T	0.72260	0.3438	L	0.55990	1.75	0.09310	N	1	P;P;P;P;P;P	0.37612	0.602;0.547;0.547;0.547;0.547;0.602	P;B;B;B;B;P	0.48524	0.58;0.444;0.444;0.444;0.444;0.58	T	0.57911	-0.7729	10	0.72032	D	0.01	.	11.1182	0.48273	0.1436:0.7209:0.1355:0.0	.	411;735;737;731;760;770	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	F	770;737;737;411	ENSP00000359489:S770F;ENSP00000359486:S737F;ENSP00000345459:S737F;ENSP00000286437:S411F	ENSP00000286437:S411F	S	+	2	0	AFF2	147845584	0.065000	0.20965	0.012000	0.15200	0.324000	0.28378	2.798000	0.47884	1.087000	0.41251	0.600000	0.82982	TCC		0.453	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2		NM_002025	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561296	32561296	+	Missense_Mutation	SNP	T	T	C	rs200111638		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr14:32561296T>C	ENST00000345122.3	+	2	1736	c.1421T>C	c.(1420-1422)gTa>gCa	p.V474A	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.V474A|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.V474A|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.V474A	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	474	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGCAAAGAGGTATATGGTAGG	0.368																																					NSCLC(9;77 350 3443 29227 41353)												0													74.0	77.0	76.0					14																	32561296		2203	4297	6500	SO:0001583	missense	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1421T>C	14.37:g.32561296T>C	ENSP00000371897:p.Val474Ala		A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311365	0.60414	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.12039	2.72;2.72;2.72;2.72	6.02	6.02	0.97574	FF domain (1);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.40543	1.245	0.80722	D	1	P;P	0.49961	0.93;0.885	P;P	0.56042	0.79;0.622	T	0.00254	-1.1874	10	0.56958	D	0.05	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	474;474	Q13017-2;Q13017	.;RHG05_HUMAN	A	474	ENSP00000452222:V474A;ENSP00000441692:V474A;ENSP00000371897:V474A;ENSP00000393307:V474A	ENSP00000371897:V474A	V	+	2	0	ARHGAP5	31631047	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.040000	0.89188	2.299000	0.77371	0.528000	0.53228	GTA		0.368	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1		NM_001030055	
ATP1B1	481	broad.mit.edu	37	1	169101269	169101270	+	3'UTR	INS	-	-	G	rs200351363|rs199593766		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:169101269_169101270insG	ENST00000367816.1	+	0	1917_1918				ATP1B1_ENST00000499679.3_3'UTR			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide						blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					tttttttttttttttttttttg	0.317																																																	0																																										SO:0001624	3_prime_UTR_variant	481			U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"""ATPases / P-type"""	804	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit beta-1"", ""sodium pump subunit beta-1"", ""sodium-potassium ATPase subunit beta 1 (non-catalytic)"""	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.*477->G	1.37:g.169101269_169101270insG			Q5TGZ3	RNA	INS	ENST00000367816.1	37	CCDS1276.1																																																																																				0.317	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			
C6orf132	647024	hgsc.bcm.edu	37	6	42075105	42075131	+	In_Frame_Del	DEL	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT	-	rs553334748|rs539692316	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr6:42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENST00000341865.4	-	4	518_544	c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	c.(517-546)ccacctcccctgctgctggaacccccaccc>ccc	p.173_182PPPLLLEPPP>P		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	173	Pro-rich.									breast(1)	1						gctgggcgggggtgggggttccagcagcaggggaggtggtgggggtg	0.665																																																	0										8,1312		4,0,656						1.1	0.5			2	76,2832		27,22,1405	no	coding	C6orf132	NM_001164446.1		31,22,2061	A1A1,A1R,RR		2.6135,0.6061,1.9868				84,4144				SO:0001651	inframe_deletion	647024				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	6.37:g.42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENSP00000341368:p.Pro173_Pro181del		A6NI05	In_Frame_Del	DEL	ENST00000341865.4	37	CCDS47428.1																																																																																				0.665	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2		NM_001164446	
CCDC124	115098	broad.mit.edu	37	19	18054506	18054506	+	Silent	SNP	C	C	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr19:18054506C>T	ENST00000597436.1	+	5	761	c.654C>T	c.(652-654)ccC>ccT	p.P218P	CCDC124_ENST00000445755.2_Silent_p.P218P	NM_138442.3	NP_612451.1	Q96CT7	CC124_HUMAN	coiled-coil domain containing 124	218					cell cycle (GO:0007049)|cell division (GO:0051301)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.P218P(1)		central_nervous_system(1)|kidney(2)	3						GGGCCGTGCCCTTCAATGCCC	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											23.0	26.0	25.0					19																	18054506		2203	4299	6502	SO:0001819	synonymous_variant	115098			BC013949	CCDS12369.1	19p13.11	2014-02-20				ENSG00000007080			25171	protein-coding gene	gene with protein product						23894443	Standard	NM_138442		Approved		uc002nhs.3	Q96CT7		ENST00000597436.1:c.654C>T	19.37:g.18054506C>T				Silent	SNP	ENST00000597436.1	37	CCDS12369.1																																																																																				0.617	CCDC124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466484.1		NM_138442	
CHD7	55636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	61754584	61754584	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr8:61754584G>A	ENST00000423902.2	+	21	5302	c.4823G>A	c.(4822-4824)aGg>aAg	p.R1608K	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1608					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R1608K(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GAATGTTTCAGGGTGGAGAAG	0.433																																																	2	Substitution - Missense(2)	kidney(2)											67.0	67.0	67.0					8																	61754584		1911	4132	6043	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4823G>A	8.37:g.61754584G>A	ENSP00000392028:p.Arg1608Lys		D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.893918	0.72639	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	T	0.68765	-0.35	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.64789	0.2630	L	0.42686	1.345	0.58432	D	0.999999	B	0.20261	0.043	B	0.27715	0.082	T	0.58885	-0.7557	10	0.44086	T	0.13	-15.3243	20.054	0.97641	0.0:0.0:1.0:0.0	.	1608	Q9P2D1	CHD7_HUMAN	K	1608	ENSP00000392028:R1608K	ENSP00000307304:R1608K	R	+	2	0	CHD7	61917138	1.000000	0.71417	0.462000	0.27118	0.997000	0.91878	9.813000	0.99286	2.808000	0.96608	0.655000	0.94253	AGG		0.433	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2		XM_098762	
CROCCP2	84809	broad.mit.edu	37	1	16944979	16944981	+	lincRNA	DEL	AAG	AAG	-	rs66601805|rs67064896|rs142983965	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:16944979_16944981delAAG	ENST00000412962.1	-	0	2538_2540				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GGATGGATAAAAGAagagcctct	0.369														946	0.188898	0.2186	0.2882	5008	,	,		72022	0.0298		0.2147	False		,,,				2504	0.2157																0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16944982_16944984delAAG			Q8NF65|Q96FR5|Q9BRE8	RNA	DEL	ENST00000412962.1	37																																																																																					0.369	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
CRYGA	1418	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	209025594	209025594	+	Missense_Mutation	SNP	C	C	G	rs201293779		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr2:209025594C>G	ENST00000304502.4	-	3	478	c.459G>C	c.(457-459)agG>agC	p.R153S		NM_014617.3	NP_055432.2	P11844	CRGA_HUMAN	crystallin, gamma A	153	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.R153S(1)		endometrium(1)|kidney(3)|large_intestine(1)|lung(7)	12				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)		AGTCGTGGTACCTTCTGTAGT	0.562																																																	1	Substitution - Missense(1)	kidney(1)											84.0	91.0	88.0					2																	209025594		2203	4300	6503	SO:0001583	missense	1418				CCDS33367.1	2q34	2013-02-14			ENSG00000168582	ENSG00000168582			2408	protein-coding gene	gene with protein product	"""gamma crystallin 5"""	123660		CRYG1			Standard	NM_014617		Approved	CRYG5, CRY-g-A		P11844	OTTHUMG00000154796	ENST00000304502.4:c.459G>C	2.37:g.209025594C>G	ENSP00000302105:p.Arg153Ser		Q53ST5	Missense_Mutation	SNP	ENST00000304502.4	37	CCDS33367.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.436906	0.25900	.	.	ENSG00000168582	ENST00000304502	T	0.73897	-0.79	4.69	-5.99	0.02213	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.235594	0.41294	D	0.000913	T	0.60405	0.2266	L	0.46614	1.455	0.09310	N	0.999998	P	0.34864	0.473	B	0.37047	0.24	T	0.55283	-0.8165	10	0.25751	T	0.34	.	10.9654	0.47410	0.0:0.2535:0.5495:0.197	.	153	P11844	CRGA_HUMAN	S	153	ENSP00000302105:R153S	ENSP00000302105:R153S	R	-	3	2	CRYGA	208733839	0.000000	0.05858	0.166000	0.22797	0.477000	0.33069	-0.899000	0.04101	-1.085000	0.03088	-0.181000	0.13052	AGG		0.562	CRYGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337096.1		NM_014617	
CSPG4	1464	broad.mit.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	C	T	rs200493777		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr15:75981976C>T	ENST00000308508.5	-	3	1522	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	477	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.			RH -> HY (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R477H(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCGCCATGGCGTGCCCCTCG	0.637																																																	1	Substitution - Missense(1)	kidney(1)											67.0	61.0	63.0					15																	75981976		2197	4291	6488	SO:0001583	missense	1464			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1430G>A	15.37:g.75981976C>T	ENSP00000312506:p.Arg477His		D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	9.517	1.107225	0.20714	.	.	ENSG00000173546	ENST00000308508	T	0.19532	2.14	5.12	4.19	0.49359	.	0.096704	0.44483	D	0.000447	T	0.17746	0.0426	L	0.57536	1.79	0.27465	N	0.953023	P	0.35628	0.513	B	0.27380	0.079	T	0.14783	-1.0460	10	0.41790	T	0.15	.	9.3594	0.38186	0.0:0.8315:0.0:0.1685	.	477	Q6UVK1	CSPG4_HUMAN	H	477	ENSP00000312506:R477H	ENSP00000312506:R477H	R	-	2	0	CSPG4	73769031	0.038000	0.19896	0.145000	0.22337	0.035000	0.12851	1.407000	0.34657	2.375000	0.81037	0.555000	0.69702	CGC		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1		NM_001897	
DDX12P	440081	broad.mit.edu	37	12	9571764	9571764	+	IGR	SNP	T	T	G	rs117821635	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr12:9571764T>G								RP13-735L24.1 (21551 upstream) : SNORA75 (25889 downstream)														p.T826T(1)									CTTCCCTGGGTGTGCCTGGCC	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											20.0	15.0	17.0					12																	9571764		625	1304	1929	SO:0001628	intergenic_variant	0																															12.37:g.9571764T>G				Missense_Mutation	SNP		37																																																																																				0	0.642									
DNAH14	127602	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	225525799	225525799	+	Intron	SNP	A	A	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:225525799A>G	ENST00000445597.2	+	46	7716				DNAH14_ENST00000430092.1_Missense_Mutation_p.I3357V|DNAH14_ENST00000439375.2_Missense_Mutation_p.I3357V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.I3357V(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CTTAAAGGCAATTCTGAAAAA	0.323																																																	1	Substitution - Missense(1)	kidney(1)											142.0	118.0	125.0					1																	225525799		692	1589	2281	SO:0001627	intron_variant	127602			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7717-162A>G	1.37:g.225525799A>G			A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.	.	.	.	.	.	.	.	.	.	A	11.22	1.575033	0.28092	.	.	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.20200	2.09;2.09	5.54	3.26	0.37387	.	0.244102	0.21256	N	0.077543	T	0.11879	0.0289	N	0.21282	0.65	0.80722	D	1	B	0.27625	0.183	B	0.30782	0.12	T	0.05801	-1.0863	10	0.06757	T	0.87	.	8.7124	0.34391	0.8409:0.0:0.1591:0.0	.	3357	Q0VDD8-4	.	V	3357	ENSP00000414402:I3357V;ENSP00000392061:I3357V	ENSP00000414402:I3357V	I	+	1	0	DNAH14	223592422	0.995000	0.38212	0.994000	0.49952	0.983000	0.72400	1.153000	0.31676	0.943000	0.37553	0.438000	0.28831	ATT		0.323	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3		XM_059166	
DST	667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	56481876	56481876	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr6:56481876T>C	ENST00000370765.6	-	24	6496	c.6389A>G	c.(6388-6390)aAc>aGc	p.N2130S	DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.N2130S(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAGAAACTTGTTAAGAGTTTT	0.438																																																	2	Substitution - Missense(2)	kidney(2)											51.0	52.0	52.0					6																	56481876		2203	4300	6503	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.6389A>G	6.37:g.56481876T>C	ENSP00000359801:p.Asn2130Ser		B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.581595	0.00879	.	.	ENSG00000151914	ENST00000370765	T	0.66638	-0.22	5.77	2.8	0.32819	.	.	.	.	.	T	0.24431	0.0592	.	.	.	0.21822	N	0.999529	B	0.02656	0.0	B	0.01281	0.0	T	0.04165	-1.0972	7	0.14252	T	0.57	.	7.8836	0.29637	0.0:0.502:0.0:0.498	.	2130	Q03001-3	.	S	2130	ENSP00000359801:N2130S	ENSP00000359801:N2130S	N	-	2	0	DST	56589835	0.813000	0.29090	0.989000	0.46669	0.626000	0.37791	1.014000	0.29950	0.352000	0.24053	-0.417000	0.06048	AAC		0.438	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2		NM_001723	
FAM71F2	346653	broad.mit.edu;ucsc.edu	37	7	128323136	128323136	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr7:128323136G>A	ENST00000480462.1	+	5	959	c.853G>A	c.(853-855)Gaa>Aaa	p.E285K	FAM71F2_ENST00000477515.1_3'UTR|FAM71F2_ENST00000378704.3_Missense_Mutation_p.E276K			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	285								p.E285K(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CAGCCTCTGGGAACAAGAGGA	0.478																																																	1	Substitution - Missense(1)	kidney(1)											46.0	44.0	45.0					7																	128323136		1921	4131	6052	SO:0001583	missense	346653			BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.853G>A	7.37:g.128323136G>A	ENSP00000420140:p.Glu285Lys		Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196381	0.38806	.	.	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001	T;T;T;T	0.12361	2.71;2.69;2.71;2.71	4.18	4.18	0.49190	.	0.000000	0.50627	D	0.000118	T	0.12008	0.0292	L	0.32530	0.975	0.34450	D	0.70061	P;P	0.43094	0.799;0.698	B;B	0.40134	0.32;0.253	T	0.16394	-1.0404	10	0.72032	D	0.01	-8.3253	12.2486	0.54585	0.0:0.0:1.0:0.0	.	276;285	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	K	276;285;276;276	ENSP00000418907:E276K;ENSP00000420140:E285K;ENSP00000367976:E276K;ENSP00000401654:E276K	ENSP00000367976:E276K	E	+	1	0	FAM71F2	128110372	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	4.060000	0.57477	2.351000	0.79841	0.558000	0.71614	GAA		0.478	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			
MROH5	389690	hgsc.bcm.edu	37	8	142459777	142459778	+	RNA	INS	-	-	A	rs144781370|rs551918924	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr8:142459777_142459778insA	ENST00000430863.1	-	0	2629_2630				SNORD5_ENST00000458800.1_RNA	NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GCAGACAGGCCAGCAGTGTGGT	0.678													A|A|AA|insertion	278	0.0555112	0.1331	0.0403	5008	,	,		17224	0.0		0.0557	False		,,,				2504	0.0184																0										474,3476		80,314,1581						3.1	0.5		dbSNP_134	17	475,7371		49,377,3497	no	frameshift	FLJ43860	NM_207414.2		129,691,5078	A1A1,A1R,RR		6.054,12.0,8.0451				949,10847						0					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142459778_142459778dupA				Frame_Shift_Ins	INS	ENST00000430863.1	37																																																																																					0.678	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4		NM_207414	
GLI2	2736	hgsc.bcm.edu;ucsc.edu	37	2	121685023	121685026	+	Frame_Shift_Del	DEL	TCTG	TCTG	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	TCTG	TCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr2:121685023_121685026delTCTG	ENST00000452319.1	+	3	295_298	c.235_238delTCTG	c.(235-240)tctgtcfs	p.SV79fs	GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Frame_Shift_Del_p.SV79fs					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CGAGCCTCATTCTGTCCACGGTGT	0.627																																																	0																																										SO:0001589	frameshift_variant	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.235_238delTCTG	2.37:g.121685023_121685026delTCTG	ENSP00000390436:p.Ser79fs			Frame_Shift_Del	DEL	ENST00000452319.1	37	CCDS33283.1																																																																																				0.627	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3		NM_005270	
RP3-470B24.5	0	broad.mit.edu	37	6	168377119	168377119	+	lincRNA	SNP	T	T	C	rs199867038		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr6:168377119T>C	ENST00000538528.1	-	0	500																											GTGGGGGTCATTCCCCCTGCA	0.622																																																	0													4.0	6.0	5.0					6																	168377119		621	1484	2105			100128124																															6.37:g.168377119T>C				Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
IGFBP6	3489	broad.mit.edu	37	12	53491636	53491638	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr12:53491636_53491638delGGA	ENST00000301464.3	+	1	408_410	c.135_137delGGA	c.(133-138)gtggag>gtg	p.E48del	IGFBP6_ENST00000548547.1_In_Frame_Del_p.E48del	NM_002178.2	NP_002169.1	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	48	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(3)|ovary(1)|pancreas(1)	6						GGGGCTGCGTGGAGGAGGAGGAT	0.719																																					Esophageal Squamous(83;1656 1718 30141 34380)												0										22,3516		9,4,1756						-4.3	0.9			4	29,6929		11,7,3461	no	coding	IGFBP6	NM_002178.2		20,11,5217	A1A1,A1R,RR		0.4168,0.6218,0.4859				51,10445				SO:0001651	inframe_deletion	3489				CCDS8846.1	12q13	2008-07-28				ENSG00000167779			5475	protein-coding gene	gene with protein product		146735				1850258, 10087296	Standard	NM_002178		Approved		uc001sbu.1	P24592	OTTHUMG00000169773	ENST00000301464.3:c.135_137delGGA	12.37:g.53491645_53491647delGGA	ENSP00000301464:p.Glu48del		Q14492	In_Frame_Del	DEL	ENST00000301464.3	37	CCDS8846.1																																																																																				0.719	IGFBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405813.1			
KIF27	55582	broad.mit.edu;hgsc.bcm.edu	37	9	86474157	86474157	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr9:86474157C>A	ENST00000297814.2	-	14	3207	c.3064G>T	c.(3064-3066)Gtc>Ttc	p.V1022F	RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000586211.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.V925F|KIF27_ENST00000413982.1_Missense_Mutation_p.V956F|RP11-575L7.4_ENST00000590417.1_RNA|RP11-575L7.4_ENST00000586206.1_RNA|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000592283.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1022					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V1022F(1)		breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TTCTGGAGGACTTCAACTTGT	0.408																																																	1	Substitution - Missense(1)	kidney(1)											227.0	197.0	207.0					9																	86474157		2202	4300	6502	SO:0001583	missense	55582			AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3064G>T	9.37:g.86474157C>A	ENSP00000297814:p.Val1022Phe		B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.239290	0.22711	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.46451	0.87;0.87;0.87	4.59	1.74	0.24563	.	0.969423	0.08452	N	0.943816	T	0.21674	0.0522	N	0.08118	0	0.09310	N	1	P;B;B	0.37636	0.603;0.432;0.257	B;B;B	0.37943	0.136;0.261;0.143	T	0.16748	-1.0392	10	0.62326	D	0.03	.	2.1161	0.03714	0.1369:0.5016:0.133:0.2285	.	925;956;1022	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	F	1022;956;925	ENSP00000297814:V1022F;ENSP00000401688:V956F;ENSP00000333928:V925F	ENSP00000297814:V1022F	V	-	1	0	KIF27	85663977	0.911000	0.30947	0.771000	0.31576	0.531000	0.34715	1.339000	0.33885	0.187000	0.20147	-1.108000	0.02087	GTC		0.408	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1		NM_017576	
LGALS9B	284194	hgsc.bcm.edu	37	17	20370782	20370783	+	Start_Codon_Ins	INS	-	-	TC	rs10687699|rs554373055|rs372509656	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr17:20370782_20370783insTC	ENST00000423676.3	-	0	64_65				LGALS9B_ENST00000324290.5_Start_Codon_Ins			Q3B8N2	LEG9B_HUMAN	lectin, galactoside-binding, soluble, 9B								carbohydrate binding (GO:0030246)	p.M1fs*12(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	10						GCTGAAGGCCATCTCCACCGCC	0.584														831	0.165935	0.2504	0.1326	5008	,	,		9041	0.127		0.1481	False		,,,				2504	0.1339																1	Insertion - Frameshift(1)	central_nervous_system(1)								372,1470		152,68,701						2.5	0.7		dbSNP_130	3	715,5069		234,247,2411	no	frameshift	LGALS9B	NM_001042685.1		386,315,3112	A1A1,A1R,RR		12.3617,20.1954,14.2539				1087,6539				SO:0001582	initiator_codon_variant	284194				CCDS42283.1	17p11.2	2011-08-04			ENSG00000170298	ENSG00000170298		"""Lectins, galactoside-binding"""	24842	protein-coding gene	gene with protein product						11997339	Standard	NM_001042685		Approved		uc002gwz.1	Q3B8N2	OTTHUMG00000130730	ENST00000423676.3:c.0_1dupGA	17.37:g.20370785_20370786dupTC			A6NLF8|A8K2J8	Frame_Shift_Ins	INS	ENST00000423676.3	37																																																																																					0.584	LGALS9B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000253230.2		NM_001042685	
MADCAM1	8174	broad.mit.edu	37	19	501762	501762	+	Missense_Mutation	SNP	A	A	C	rs200007467		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr19:501762A>C	ENST00000215637.3	+	4	807	c.761A>C	c.(760-762)cAg>cCg	p.Q254P	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.Q35P	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	254	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.			Q -> P (in Ref. 1; AAC13661). {ECO:0000305}.	aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)	p.Q254P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCAGGAGCCTCCC	0.721																																																	1	Substitution - Missense(1)	kidney(1)											31.0	36.0	34.0					19																	501762		2194	4290	6484	SO:0001583	missense	8174			U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.761A>C	19.37:g.501762A>C	ENSP00000215637:p.Gln254Pro		A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	N	5.739	0.320845	0.10845	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.09073	3.02	2.86	-5.72	0.02406	.	.	.	.	.	T	0.01940	0.0061	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	9	0.02654	T	1	.	3.6031	0.08032	0.3032:0.5048:0.0:0.192	.	254	Q13477	MADCA_HUMAN	P	278;270;262;254	ENSP00000215637:Q254P	ENSP00000215637:Q254P	Q	+	2	0	MADCAM1	452762	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.356000	0.00247	-1.159000	0.02807	-1.988000	0.00451	CAG		0.721	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1		NM_130760	
LILRB1	10859	broad.mit.edu;hgsc.bcm.edu	37	19	55143551	55143551	+	Missense_Mutation	SNP	G	G	A	rs112916853	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr19:55143551G>A	ENST00000396331.1	+	6	881	c.524G>A	c.(523-525)cGt>cAt	p.R175H	LILRB1_ENST00000448689.1_Missense_Mutation_p.R175H|LILRB1_ENST00000396321.2_Missense_Mutation_p.R175H|LILRB1_ENST00000418536.2_Missense_Mutation_p.R175H|LILRB1_ENST00000396327.3_Missense_Mutation_p.R175H|LILRB1_ENST00000396315.1_Missense_Mutation_p.R175H|LILRB1_ENST00000396332.4_Missense_Mutation_p.R175H|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000434867.2_Missense_Mutation_p.R175H|LILRB1_ENST00000396317.1_Missense_Mutation_p.R175H|LILRB1_ENST00000427581.2_Missense_Mutation_p.R211H|LILRB1_ENST00000324602.7_Missense_Mutation_p.R175H	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	175	Ig-like C2-type 2.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.R175H(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCCCATGCCCGTGGGTCGTCC	0.577										HNSCC(37;0.09)																																							1	Substitution - Missense(1)	kidney(1)											137.0	131.0	133.0					19																	55143551		2203	4300	6503	SO:0001583	missense	10859			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.524G>A	19.37:g.55143551G>A	ENSP00000379622:p.Arg175His		A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	4.485	0.089986	0.08632	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93;3.93;3.93;3.93;3.93;3.93;3.93	1.48	-2.96	0.05547	Immunoglobulin-like fold (1);	2.505650	0.01251	N	0.008883	T	0.03695	0.0105	L	0.37630	1.12	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.002;0.003;0.001;0.006	B;B;B;B;B	0.09377	0.002;0.002;0.004;0.002;0.004	T	0.39840	-0.9594	10	0.40728	T	0.16	.	3.5547	0.07860	0.4806:0.2081:0.3112:0.0	.	175;175;175;175;175	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	H	175;175;175;175;175;175;175;175;211;175;175	ENSP00000379614:R175H;ENSP00000391514:R175H;ENSP00000409968:R175H;ENSP00000379622:R175H;ENSP00000379618:R175H;ENSP00000315997:R175H;ENSP00000405243:R175H;ENSP00000379623:R175H;ENSP00000395004:R211H;ENSP00000379610:R175H;ENSP00000379608:R175H	ENSP00000315997:R175H	R	+	2	0	LILRB1	59835363	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.471000	0.00990	-1.525000	0.01762	-1.139000	0.01908	CGT		0.577	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			
MSI1	4440	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	120791103	120791103	+	Splice_Site	SNP	G	G	A	rs140182426		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr12:120791103G>A	ENST00000257552.2	-	10	820	c.732C>T	c.(730-732)ccC>ccT	p.P244P	MSI1_ENST00000546622.1_5'Flank	NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	244					epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)	p.P244P(1)		breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGACTTACCGGGGAACTGGT	0.617																																																	1	Substitution - coding silent(1)	kidney(1)						G		1,4405	2.1+/-5.4	0,1,2202	139.0	135.0	136.0		732	-1.1	1.0	12	dbSNP_134	136	0,8600		0,0,4300	no	coding-synonymous-near-splice	MSI1	NM_002442.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		244/363	120791103	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	4440			AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	7330	protein-coding gene	gene with protein product		603328	"""Musashi (Drosophila) homolog 1"", ""musashi homolog 1 (Drosophila)"""			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.733+1C>T	12.37:g.120791103G>A			Q96PU0|Q96PU1|Q96PU2|Q96PU3	Silent	SNP	ENST00000257552.2	37	CCDS9196.1	.	.	.	.	.	.	.	.	.	.	G	8.391	0.839685	0.16891	2.27E-4	0.0	ENSG00000135097	ENST00000546985	T	0.42900	0.96	4.77	-1.11	0.09840	.	0.000000	0.64402	D	0.000005	T	0.43831	0.1265	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29761	-1.0001	7	0.45353	T	0.12	.	7.9032	0.29746	0.3472:0.0:0.5405:0.1122	.	.	.	.	L	176	ENSP00000446710:P176L	ENSP00000446710:P176L	P	-	2	0	MSI1	119275486	0.001000	0.12720	0.997000	0.53966	0.674000	0.39518	-1.148000	0.03185	-0.139000	0.11414	-1.360000	0.01215	CCG		0.617	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1		NM_002442	Silent
Unknown	0	broad.mit.edu	37	1	16976345	16976345	+	IGR	SNP	T	T	C	rs200927593	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:16976345T>C								CROCCP2 (15291 upstream) : RNU1-3 (16934 downstream)																							CCTTGCTGAATGTCATCTCCA	0.582													.|||	1651	0.329673	0.4395	0.2522	5008	,	,		33305	0.5784		0.174	False		,,,				2504	0.1401																0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16976345T>C				RNA	SNP		37																																																																																				0	0.582									
MUC4	4585	broad.mit.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr3:195506555C>T	ENST00000463781.3	-	2	12355	c.11896G>A	c.(11896-11898)Gcc>Acc	p.A3966T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3966T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3966T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													.|||	176	0.0351438	0.0083	0.0677	5008	,	,		7977	0.0119		0.0915	False		,,,				2504	0.0143																2	Substitution - Missense(2)	endometrium(1)|kidney(1)											15.0	10.0	11.0					3																	195506555		666	1488	2154	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11896G>A	3.37:g.195506555C>T	ENSP00000417498:p.Ala3966Thr		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.905	-0.721125	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48522	1.23;0.81	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.12915	-1.0529	7	.	.	.	-3.1782	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	.	3838	E7ESK3	.	T	3966	ENSP00000417498:A3966T;ENSP00000420243:A3966T	.	A	-	1	0	MUC4	196991334	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.202000	0.09451	-2.037000	0.00920	-2.088000	0.00374	GCC		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195509031	195509078	+	In_Frame_Del	DEL	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	-	rs540650529|rs78565605|rs559337249|rs75721951|rs35479616|rs35658525|rs201338210|rs371017154|rs75309583|rs77818558|rs71634715|rs185913520|rs35533324	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr3:195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENST00000463781.3	-	2	9832_9879	c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	c.(9373-9420)gacacttcctcagcatccacaggtcaggccaccgctcttcctgtcaccdel	p.DTSSASTGQATALPVT3125del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.DTSSASTGQATALPVT3125del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGCTGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGGTGACAGGA	0.593																																																	0																																										SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	3.37:g.195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENSP00000417498:p.Asp3125_Thr3140del		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.593	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195509394	195509394	+	Silent	SNP	T	T	G	rs377471271	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr3:195509394T>G	ENST00000463781.3	-	2	9516	c.9057A>C	c.(9055-9057)acA>acC	p.T3019T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3019T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3019T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGCGTGACCTGTGGATATTG	0.592													.|||	899	0.179513	0.2345	0.1311	5008	,	,		9893	0.0605		0.2575	False		,,,				2504	0.182																1	Substitution - coding silent(1)	kidney(1)											24.0	19.0	20.0					3																	195509394		663	1570	2233	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9057A>C	3.37:g.195509394T>G			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MZT1	440145	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	73293134	73293134	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr13:73293134A>C	ENST00000377818.3	-	2	265	c.181T>G	c.(181-183)Tca>Gca	p.S61A		NM_001071775.2	NP_001065243.1	Q08AG7	MZT1_HUMAN	mitotic spindle organizing protein 1	61					gamma-tubulin complex localization (GO:0033566)	centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)		p.S61A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						ATAACCGATGATAAAGCTTCT	0.353																																																	1	Substitution - Missense(1)	kidney(1)											112.0	118.0	116.0					13																	73293134		2203	4300	6503	SO:0001583	missense	440145				CCDS31990.1	13q22.1	2013-08-13	2010-07-22	2010-07-22	ENSG00000204899	ENSG00000204899			33830	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1"""	613448	"""chromosome 13 open reading frame 37"""	C13orf37		20360068	Standard	NM_001071775		Approved	LOC440145, FLJ21869, MGC150539, RP11-11C5.2, MOZART1	uc001viu.2	Q08AG7	OTTHUMG00000017069	ENST00000377818.3:c.181T>G	13.37:g.73293134A>C	ENSP00000367049:p.Ser61Ala		Q5W0P5	Missense_Mutation	SNP	ENST00000377818.3	37	CCDS31990.1	.	.	.	.	.	.	.	.	.	.	A	9.098	1.003350	0.19121	.	.	ENSG00000204899	ENST00000377818	T	0.26660	1.72	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	.	.	.	0.58432	D	0.999997	P	0.49185	0.92	D	0.64042	0.921	T	0.05599	-1.0875	9	0.02654	T	1	-15.0368	15.9666	0.79979	1.0:0.0:0.0:0.0	.	61	Q08AG7	MZT1_HUMAN	A	61	ENSP00000367049:S61A	ENSP00000367049:S61A	S	-	1	0	MZT1	72191135	1.000000	0.71417	0.990000	0.47175	0.969000	0.65631	6.884000	0.75600	2.174000	0.68829	0.482000	0.46254	TCA		0.353	MZT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045249.1		NM_001071775	
NBPF12	149013	broad.mit.edu	37	1	146398399	146398399	+	Missense_Mutation	SNP	G	G	A	rs377655940	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:146398399G>A	ENST00000442909.2	+	7	1221	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	NBPF12_ENST00000309471.8_Missense_Mutation_p.A54T|NBPF12_ENST00000446760.2_Missense_Mutation_p.A129T			Q5TAG4	NBPFC_HUMAN	neuroblastoma breakpoint family, member 12	0	NBPF 2. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.A129T(2)		ovary(2)	2						GCATCTCCAGGCCCTCCTCAC	0.562													.|||	473	0.0944489	0.0582	0.1297	5008	,	,		20533	0.1925		0.0795	False		,,,				2504	0.0327																2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	100132406			BG154169	CCDS72881.1	1q21.1	2013-01-17	2011-06-28	2011-06-28	ENSG00000186275	ENSG00000268043		"""neuroblastoma breakpoint family"""	24297	protein-coding gene	gene with protein product		608607	"""KIAA1245"""	KIAA1245		11948409	Standard	NM_001278141		Approved	COAS1		Q5TAG4	OTTHUMG00000043708	ENST00000442909.2:c.385G>A	1.37:g.146398399G>A	ENSP00000391116:p.Ala129Thr		O95877	Missense_Mutation	SNP	ENST00000442909.2	37		.	.	.	.	.	.	.	.	.	.	N	10.47	1.358065	0.24598	.	.	ENSG00000186275	ENST00000446760;ENST00000442909;ENST00000309471	T;T;T	0.42513	4.12;4.12;0.97	1.68	-1.18	0.09617	.	.	.	.	.	T	0.20861	0.0502	L	0.52759	1.655	0.80722	P	0.0	P	0.46395	0.877	P	0.51866	0.682	T	0.06267	-1.0836	8	0.21014	T	0.42	.	2.9871	0.05971	0.2025:0.2889:0.5085:0.0	.	129	Q86T75-2	.	T	129;129;54	ENSP00000396525:A129T;ENSP00000391116:A129T;ENSP00000311131:A54T	ENSP00000311131:A54T	A	+	1	0	NBPF12	144765764	0.004000	0.15560	0.000000	0.03702	0.063000	0.16089	0.761000	0.26489	-0.391000	0.07763	0.361000	0.22055	GCC		0.562	NBPF12-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000102086.3		XM_003119146	
NEFH	4744	hgsc.bcm.edu	37	22	29885580	29885581	+	In_Frame_Ins	INS	-	-	AGGCCAAGTCCCCTGAGA	rs200984527|rs267607533		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr22:29885580_29885581insAGGCCAAGTCCCCTGAGA	ENST00000310624.6	+	4	1984_1985	c.1951_1952insAGGCCAAGTCCCCTGAGA	c.(1951-1953)aag>aAGGCCAAGTCCCCTGAGAag	p.651_651K>KAKSPEK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	657	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GTCCCCTGAGAAGGCCAAGTCC	0.569																																																	0																																										SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	22.37:g.29885580_29885581insAGGCCAAGTCCCCTGAGA	ENSP00000311997:p.AlaLysSerProGluLys657dup		B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2		NM_021076	
NIPA2	81614	hgsc.bcm.edu	37	15	23006304	23006304	+	Missense_Mutation	SNP	T	T	C	rs201538213		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr15:23006304T>C	ENST00000337451.3	-	8	1612	c.1000A>G	c.(1000-1002)Aat>Gat	p.N334D	NIPA2_ENST00000398014.2_Missense_Mutation_p.N334D|NIPA2_ENST00000359727.4_Missense_Mutation_p.N315D|NIPA2_ENST00000398013.3_Missense_Mutation_p.N334D|NIPA2_ENST00000539711.2_Missense_Mutation_p.N315D	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	334						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		CTTTCTTCATTATTATTAAGA	0.368																																																	0													58.0	61.0	60.0					15																	23006304		2203	4300	6503	SO:0001583	missense	81614			AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.1000A>G	15.37:g.23006304T>C	ENSP00000337618:p.Asn334Asp		F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	37	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	T	9.597	1.127681	0.20959	.	.	ENSG00000140157	ENST00000337451;ENST00000398014;ENST00000359727;ENST00000539711;ENST00000398013	D;D;D	0.89875	-2.58;-2.58;-2.58	5.16	2.6	0.31112	.	0.998104	0.08119	N	0.995053	T	0.73249	0.3563	N	0.08118	0	0.27494	N	0.952199	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.61083	-0.7134	10	0.05959	T	0.93	-5.5444	5.9858	0.19434	0.0:0.4898:0.0:0.5102	.	315;334	F8W7Y8;Q8N8Q9	.;NIPA2_HUMAN	D	334;334;315;334;315	ENSP00000337618:N334D;ENSP00000381096:N334D;ENSP00000352762:N315D	ENSP00000337618:N334D	N	-	1	0	NIPA2	20557745	0.945000	0.32115	0.992000	0.48379	0.990000	0.78478	0.739000	0.26173	0.779000	0.33543	0.456000	0.33151	AAT		0.368	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1		NM_030922	
NPC1	4864	broad.mit.edu;ucsc.edu|broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	21141440	21141441	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx|Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr18:21141440_21141441GC>TT	ENST00000269228.5	-	5	1068_1069	c.514_515GC>AA	c.(514-516)GCc>AAc	p.A172N	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_5'Flank	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	172					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)	p.A172T(1)|p.A172D(1)		breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GAGTCCCAGGGCCTTGTCATTA	0.49																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	4864			AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.514_515delinsTT	18.37:g.21141440_21141441delinsTT	ENSP00000269228:p.Ala172Asn		B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																				0.490	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2		NM_000271	
NPRL2	10641	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	50386816	50386816	+	Splice_Site	SNP	C	C	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr3:50386816C>G	ENST00000232501.3	-	4	887		c.e4+1		ZMYND10_ENST00000231749.3_5'Flank|NPRL2_ENST00000493465.1_5'Flank|CYB561D2_ENST00000424512.1_5'Flank|CYB561D2_ENST00000232508.5_5'Flank|CYB561D2_ENST00000418577.1_5'Flank|XXcos-LUCA11.5_ENST00000606589.1_5'Flank|CYB561D2_ENST00000425346.1_5'Flank	NM_006545.4	NP_006536.3	Q8WTW4	NPRL2_HUMAN	nitrogen permease regulator-like 2 (S. cerevisiae)						negative regulation of kinase activity (GO:0033673)|protein phosphorylation (GO:0006468)		GTPase activator activity (GO:0005096)|protein kinase activity (GO:0004672)	p.?(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	11						GCTGGCCATACCAATGGGCAG	0.552																																																	1	Unknown(1)	kidney(1)											70.0	59.0	63.0					3																	50386816		2203	4300	6503	SO:0001630	splice_region_variant	10641			AF040708	CCDS2826.1	3p21.3	2010-03-30	2010-03-30	2010-03-30	ENSG00000114388	ENSG00000114388			24969	protein-coding gene	gene with protein product		607072	"""tumor suppressor candidate 4"""	TUSC4		11085536	Standard	NM_006545		Approved	NPR2L, NPR2	uc003daj.1	Q8WTW4	OTTHUMG00000156864	ENST00000232501.3:c.448+1G>C	3.37:g.50386816C>G			A8K831|Q6FGS2|Q9Y249|Q9Y497	Splice_Site	SNP	ENST00000232501.3	37	CCDS2826.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.294934	0.23564	.	.	ENSG00000114388	ENST00000232501	.	.	.	5.54	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7491	0.77969	0.1377:0.8623:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NPRL2	50361820	1.000000	0.71417	0.990000	0.47175	0.209000	0.24338	7.722000	0.84778	1.323000	0.45263	-0.182000	0.12963	.		0.552	NPRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346299.1		NM_006545	Intron
OR2C1	4993	hgsc.bcm.edu	37	16	3406757	3406757	+	Frame_Shift_Del	DEL	T	T	-	rs142397376	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr16:3406757delT	ENST00000304936.2	+	1	869	c.817delT	c.(817-819)ttcfs	p.F273fs		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	273					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CCAGGGCAAGTTCATTTCCCT	0.552													TT|TT|T|deletion	158	0.0315495	0.003	0.0403	5008	,	,		20105	0.0179		0.0716	False		,,,				2504	0.0368																0										43,4215		0,43,2086	99.0	79.0	86.0			-5.8	0.7	16	dbSNP_134	91	496,7756		11,474,3641	no	frameshift	OR2C1	NM_012368.2		11,517,5727	A1A1,A1R,RR		6.0107,1.0099,4.3086			3406757	539,11971	2197	4299	6496	SO:0001589	frameshift_variant	4993			AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"""GPCR / Class A : Olfactory receptors"""	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.817delT	16.37:g.3406757delT	ENSP00000307726:p.Phe273fs		A0AVA4|Q6IF34|Q6IF55	Frame_Shift_Del	DEL	ENST00000304936.2	37	CCDS10502.1																																																																																				0.552	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3			
OR5W2	390148	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	55681849	55681849	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr11:55681849A>T	ENST00000344514.1	-	1	209	c.210T>A	c.(208-210)gaT>gaA	p.D70E		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D70E(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AATAGCAGAGATCACAGAAAG	0.403																																					Melanoma(48;171 1190 15239 43886 49348)												1	Substitution - Missense(1)	kidney(1)											126.0	120.0	122.0					11																	55681849		2201	4296	6497	SO:0001583	missense	390148			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.210T>A	11.37:g.55681849A>T	ENSP00000342448:p.Asp70Glu			Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.310161	0.60414	.	.	ENSG00000187612	ENST00000344514	T	0.01152	5.26	5.01	0.987	0.19790	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000720	T	0.02649	0.0080	L	0.48362	1.52	0.29316	N	0.867677	D	0.67145	0.996	P	0.59487	0.858	T	0.27400	-1.0075	10	0.87932	D	0	.	7.3768	0.26833	0.5049:0.0:0.4951:0.0	.	70	Q8NH69	OR5W2_HUMAN	E	70	ENSP00000342448:D70E	ENSP00000342448:D70E	D	-	3	2	OR5W2	55438425	0.000000	0.05858	0.938000	0.37757	0.532000	0.34746	-0.462000	0.06704	-0.084000	0.12595	-0.384000	0.06662	GAT		0.403	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1		NM_001001960	
PGLYRP3	114771	broad.mit.edu;ucsc.edu	37	1	153275057	153275057	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr1:153275057C>A	ENST00000290722.1	-	5	608	c.556G>T	c.(556-558)Gct>Tct	p.A186S		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	186					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.A186S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCTTCCCAAGCAGATCGTTTG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											208.0	204.0	205.0					1																	153275057		2203	4300	6503	SO:0001583	missense	114771			AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.556G>T	1.37:g.153275057C>A	ENSP00000290722:p.Ala186Ser		A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	C	8.199	0.797782	0.16327	.	.	ENSG00000159527	ENST00000290722	T	0.16743	2.32	4.49	-1.39	0.08997	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (2);	0.596926	0.15853	N	0.241425	T	0.03263	0.0095	L	0.39397	1.21	0.09310	N	1	B	0.06786	0.001	B	0.21917	0.037	T	0.42310	-0.9459	10	0.25106	T	0.35	-24.4715	2.9246	0.05780	0.3548:0.3436:0.0:0.3016	.	186	Q96LB9	PGRP3_HUMAN	S	186	ENSP00000290722:A186S	ENSP00000290722:A186S	A	-	1	0	PGLYRP3	151541681	0.000000	0.05858	0.579000	0.28588	0.783000	0.44284	-1.073000	0.03430	-0.069000	0.12931	0.655000	0.94253	GCT		0.468	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1		NM_052891	
PLOD3	8985	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	100860059	100860060	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr7:100860059_100860060GC>TA	ENST00000223127.3	-	2	515_516	c.117_118GC>TA	c.(115-120)ctGCtg>ctTAtg	p.L40M	ZNHIT1_ENST00000305105.2_5'Flank	NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	40					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)	p.L44M(1)|p.L39L(1)|p.L40M(1)|p.L43L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	GTGATCACCAGCAGCTTCTCTG	0.589																																																	4	Substitution - Missense(2)|Substitution - coding silent(2)	kidney(4)																																								SO:0001583	missense	8985			AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"""lysyl hydroxlase 3"""	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.117_118delinsTA	7.37:g.100860059_100860060delinsTA	ENSP00000223127:p.Leu40Met		B2R6W6|Q540C3	Missense_Mutation|Silent	SNP	ENST00000223127.3	37	CCDS5715.1																																																																																				0.589	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1			
RBM39	9584	broad.mit.edu;ucsc.edu	37	20	34319917	34319917	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr20:34319917C>T	ENST00000253363.6	-	4	265	c.242G>A	c.(241-243)cGg>cAg	p.R81Q	RBM39_ENST00000361162.6_Missense_Mutation_p.R81Q|RBM39_ENST00000528062.3_Missense_Mutation_p.R81Q|RBM39_ENST00000407261.4_5'UTR			Q14498	RBM39_HUMAN	RNA binding motif protein 39	81	Arg/Ser-rich (RS domain).				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R81Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TGAGCGGCTCCGTCGCCTCTC	0.438																																																	1	Substitution - Missense(1)	kidney(1)											182.0	175.0	177.0					20																	34319917		2203	4300	6503	SO:0001583	missense	9584			L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"""RNA binding motif (RRM) containing"""	15923	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen receptors"", ""functional spliceosome-associated protein 59"""	604739	"""RNA-binding region (RNP1, RRM) containing 2"""	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.242G>A	20.37:g.34319917C>T	ENSP00000253363:p.Arg81Gln		A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Missense_Mutation	SNP	ENST00000253363.6	37	CCDS13266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	24.3|24.3	4.515348|4.515348	0.85389|0.85389	.|.	.|.	ENSG00000131051|ENSG00000131051	ENST00000426951|ENST00000253363;ENST00000361162;ENST00000528062;ENST00000374038;ENST00000427743;ENST00000434927	.|T;T;T;T;T;T	.|0.64260	.|2.7;2.7;-0.09;1.99;1.99;0.22	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|0.054440	.|0.64402	.|D	.|0.000001	T|T	0.60625|0.60625	0.2283|0.2283	M|M	0.76002|0.76002	2.32|2.32	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.32731	.|0.196;0.196;0.296;0.196;0.382	.|B;B;B;B;B	.|0.25291	.|0.016;0.027;0.059;0.027;0.027	T|T	0.63211|0.63211	-0.6688|-0.6688	5|10	.|0.54805	.|T	.|0.06	.|.	13.4701|13.4701	0.61278|0.61278	0.0:0.9291:0.0:0.0709|0.0:0.9291:0.0:0.0709	.|.	.|81;81;81;81;57	.|B4DRA0;A2RRD3;Q14498-2;Q14498;B3KWX7	.|.;.;.;RBM39_HUMAN;.	R|Q	69|81	.|ENSP00000253363:R81Q;ENSP00000354437:R81Q;ENSP00000436747:R81Q;ENSP00000363150:R81Q;ENSP00000406801:R81Q;ENSP00000393493:R81Q	.|ENSP00000253363:R81Q	G|R	-|-	1|2	0|0	RBM39|RBM39	33783331|33783331	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	5.561000|5.561000	0.67339|0.67339	2.789000|2.789000	0.95967|0.95967	0.651000|0.651000	0.88453|0.88453	GGA|CGG		0.438	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2		NM_184237	
RGAG1	57529	hgsc.bcm.edu	37	X	109696032	109696032	+	Silent	SNP	A	A	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chrX:109696032A>G	ENST00000465301.2	+	3	2433	c.2187A>G	c.(2185-2187)ggA>ggG	p.G729G	RGAG1_ENST00000540313.1_Silent_p.G729G	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	729										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						AAGATCCTGGAGGGATGTCCA	0.522																																																	0													142.0	119.0	126.0					X																	109696032		2203	4300	6503	SO:0001819	synonymous_variant	57529			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2187A>G	X.37:g.109696032A>G			Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																				0.522	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2		NM_020769	
SCAF1	58506	hgsc.bcm.edu	37	19	50154270	50154271	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr19:50154270_50154271insC	ENST00000360565.3	+	7	748_749	c.624_625insC	c.(625-627)cccfs	p.P209fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	209	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		ccccttcccctcccccaccccc	0.703																																																	0																																										SO:0001589	frameshift_variant	58506			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.629dupC	19.37:g.50154275_50154275dupC	ENSP00000353769:p.Pro209fs		Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Ins	INS	ENST00000360565.3	37	CCDS33074.1																																																																																				0.703	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1		NM_021228	
SCPEP1	59342	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	55058513	55058513	+	Silent	SNP	C	C	G	rs376140010		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr17:55058513C>G	ENST00000262288.3	+	2	202	c.147C>G	c.(145-147)gcC>gcG	p.A49A	RP5-1107A17.4_ENST00000572877.1_RNA|SCPEP1_ENST00000571898.1_3'UTR	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	49					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)	p.A49A(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					GCAAGGATGCCTACATGTTCT	0.512																																																	1	Substitution - coding silent(1)	kidney(1)											145.0	117.0	126.0					17																	55058513		2203	4300	6503	SO:0001819	synonymous_variant	59342			AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.147C>G	17.37:g.55058513C>G			Q96A94|Q9H3F0	Silent	SNP	ENST00000262288.3	37	CCDS11593.1																																																																																				0.512	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1		NM_021626	
SEMA3A	10371	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	83640554	83640554	+	Silent	SNP	A	A	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr7:83640554A>G	ENST00000265362.4	-	8	1184	c.870T>C	c.(868-870)cgT>cgC	p.R290R	SEMA3A_ENST00000436949.1_Silent_p.R290R	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	290	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.R290R(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						AGCAAATCAGACGAGCTTTGA	0.403																																																	1	Substitution - coding silent(1)	kidney(1)											134.0	123.0	127.0					7																	83640554		2203	4300	6503	SO:0001819	synonymous_variant	10371			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.870T>C	7.37:g.83640554A>G				Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																				0.403	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2		NM_006080	
SLC16A9	220963	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	61432539	61432539	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr10:61432539C>G	ENST00000395348.3	-	3	965	c.329G>C	c.(328-330)gGc>gCc	p.G110A	SLC16A9_ENST00000395347.1_Missense_Mutation_p.G110A	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	110					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.G110A(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						TACAACAATGCCATAGGAAAA	0.428																																																	1	Substitution - Missense(1)	kidney(1)											95.0	88.0	90.0					10																	61432539		2203	4300	6503	SO:0001583	missense	220963			AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.329G>C	10.37:g.61432539C>G	ENSP00000378757:p.Gly110Ala		Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922515	0.92319	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.77098	-1.07;-1.07	5.84	5.84	0.93424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.093725	0.64402	D	0.000001	D	0.89653	0.6777	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89742	0.3934	10	0.62326	D	0.03	.	20.1392	0.98050	0.0:1.0:0.0:0.0	.	110	Q7RTY1	MOT9_HUMAN	A	110	ENSP00000378757:G110A;ENSP00000378756:G110A	ENSP00000378756:G110A	G	-	2	0	SLC16A9	61102545	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.433000	0.80362	2.775000	0.95449	0.655000	0.94253	GGC		0.428	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2		NM_194298	
SOBP	55084	broad.mit.edu;ucsc.edu	37	6	107811866	107811866	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr6:107811866A>G	ENST00000317357.5	+	1	705	c.46A>G	c.(46-48)Agc>Ggc	p.S16G		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)									p.S16G(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		AAATAAACGGAGCAGGAAGCC	0.537																																																	1	Substitution - Missense(1)	kidney(1)											53.0	63.0	60.0					6																	107811866		1861	4106	5967	SO:0001583	missense	55084			AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.46A>G	6.37:g.107811866A>G	ENSP00000318900:p.Ser16Gly			Missense_Mutation	SNP	ENST00000317357.5	37	CCDS43488.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.052105	0.75960	.	.	ENSG00000112320	ENST00000317357	T	0.11821	2.74	4.9	3.71	0.42584	.	0.000000	0.85682	U	0.000000	T	0.05502	0.0145	L	0.38175	1.15	0.50632	D	0.999882	B	0.12630	0.006	B	0.16722	0.016	T	0.08534	-1.0717	10	0.72032	D	0.01	-11.0105	10.7341	0.46115	0.9224:0.0:0.0775:0.0	.	16	A7XYQ1	SOBP_HUMAN	G	16	ENSP00000318900:S16G	ENSP00000318900:S16G	S	+	1	0	SOBP	107918559	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.564000	0.90726	1.831000	0.53308	0.379000	0.24179	AGC		0.537	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2		NM_018013	
LOC101927040	101927040	broad.mit.edu	37	8	80783815	80783816	+	lincRNA	INS	-	-	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr8:80783815_80783816insT	ENST00000502766.2	-	0	156_157																											TGGGAGTAGCCTTTGACACAGT	0.599																																																	0																																												0																															8.37:g.80783818_80783818dupT				RNA	INS	ENST00000502766.2	37																																																																																					0.599	RP11-26J3.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000379270.1			
ZCCHC14	23174	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	87493617	87493621	+	Frame_Shift_Del	DEL	TGCTG	TGCTG	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	TGCTG	TGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr16:87493617_87493621delTGCTG	ENST00000268616.4	-	2	493_497	c.276_280delCAGCA	c.(274-282)cacagcaaafs	p.HSK92fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	92							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CACTCACCTTTGCTGTGTTTTCCTA	0.551																																																	0																																										SO:0001589	frameshift_variant	23174			AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.276_280delCAGCA	16.37:g.87493617_87493621delTGCTG	ENSP00000268616:p.His92fs		D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	37	CCDS10961.1																																																																																				0.551	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1		NM_015144	
ZFHX3	463	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	72831125	72831125	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr16:72831125C>A	ENST00000268489.5	-	9	6128	c.5456G>T	c.(5455-5457)aGt>aTt	p.S1819I	ZFHX3_ENST00000397992.5_Missense_Mutation_p.S905I	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1819					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S1819I(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CAGTGCCCCACTGGTCACTGG	0.592																																																	1	Substitution - Missense(1)	kidney(1)											87.0	82.0	84.0					16																	72831125		2198	4300	6498	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5456G>T	16.37:g.72831125C>A	ENSP00000268489:p.Ser1819Ile		D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.913831	0.33815	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.73789	-0.78;-0.76	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000015	T	0.63510	0.2517	N	0.24115	0.695	0.53005	D	0.999966	P	0.35077	0.483	B	0.27887	0.084	T	0.63470	-0.6630	10	0.46703	T	0.11	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	1819	Q15911	ZFHX3_HUMAN	I	1819;905	ENSP00000268489:S1819I;ENSP00000438926:S905I	ENSP00000268489:S1819I	S	-	2	0	ZFHX3	71388626	0.994000	0.37717	0.966000	0.40874	0.929000	0.56500	3.192000	0.50989	2.854000	0.98071	0.655000	0.94253	AGT		0.592	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1		NM_006885	
ZFHX3	463	hgsc.bcm.edu	37	16	72992581	72992581	+	Missense_Mutation	SNP	G	G	T	rs143031716|rs572247038|rs376713069	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chr16:72992581G>T	ENST00000268489.5	-	2	2136	c.1464C>A	c.(1462-1464)gaC>gaA	p.D488E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	488	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGCAACcctcgtcttcctcct	0.592																																																	0													62.0	67.0	65.0					16																	72992581		2198	4300	6498	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1464C>A	16.37:g.72992581G>T	ENSP00000268489:p.Asp488Glu		D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	0.128	-1.117039	0.01799	.	.	ENSG00000140836	ENST00000268489	T	0.74315	-0.83	5.01	-4.54	0.03452	.	0.372485	0.18321	N	0.144801	T	0.40979	0.1139	N	0.08118	0	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.43507	-0.9387	10	0.02654	T	1	.	7.313	0.26485	0.3631:0.4683:0.1686:0.0	.	488	Q15911	ZFHX3_HUMAN	E	488	ENSP00000268489:D488E	ENSP00000268489:D488E	D	-	3	2	ZFHX3	71550082	0.003000	0.15002	0.963000	0.40424	0.195000	0.23768	-1.237000	0.02922	-0.563000	0.06078	-0.802000	0.03209	GAC		0.592	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1		NM_006885	
ZNF185	7739	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	152086678	152086678	+	Silent	SNP	C	C	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa	18405e90-5663-4bf6-a93e-eb84613a8d4c	g.chrX:152086678C>T	ENST00000370268.4	+	6	448	c.411C>T	c.(409-411)acC>acT	p.T137T	ZNF185_ENST00000370270.2_Silent_p.T137T|ZNF185_ENST00000539731.1_Silent_p.T137T|ZNF185_ENST00000324823.6_Silent_p.T2T|ZNF185_ENST00000535861.1_Silent_p.T137T|ZNF185_ENST00000318529.8_Silent_p.T2T|ZNF185_ENST00000318504.7_Silent_p.T137T|ZNF185_ENST00000449285.2_Silent_p.T137T			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	137						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.T137T(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					ACAAGATGACCACTGAGGATT	0.557																																																	1	Substitution - coding silent(1)	kidney(1)											58.0	62.0	60.0					X																	152086678		2074	4178	6252	SO:0001819	synonymous_variant	7739			AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"""Zinc fingers, C2H2-type"""	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.411C>T	X.37:g.152086678C>T			A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Silent	SNP	ENST00000370268.4	37	CCDS48184.1																																																																																				0.557	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1		NM_007150	
